Force Field Analysis

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root mean square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G*results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, respectively), which were parameterized to these basepairs.

Apparently a straightforward elaboration of anatomical difference, “gender”; is symbolically tied to many kinds of cultural representations, which, in turn, set the terms not only for understanding the relations between women and men but for organizing self‐experience. Consequently, problems of self may come to be coded in terms of gender, and those of gender, in terms of the self. Using a clinical example, I speak of gender less as a determinate category than as something resembling a force field, that is, as a set of complex and shifting relations among multiple contrasts or differences. This multiplicity, in turn, generates some technical recommendations about gender and splitting. Recapturing split‐off parts of the self therefore requires inhabiting its transitional spaces, including that in which gender is not a given but is in question. Moreover, I suggest, counterintuitively, that gender identity both seals the package of self and preserves all the self must lose and thus bridges undifferentiated archaic depths and selfhood. In transference and countertransference, both patient and analyst must also enter this paradoxical space, where they alternate between being gendered and being gender‐free.

To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relationship between bond distance and bond order on one hand and between bond order and bond energy on the other hand that leads to proper dissociation of bonds to separated atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become constant as R ij f 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chemical calculations on bond dissociation and reactions of small molecules plus heat of formation and geometry data for a number of stable hydrocarbon compounds. We find that the ReaxFF provides a good description of these data. Generally, the results are of an accuracy similar or better than PM3, while ReaxFF is about 100 times faster. In turn, the PM3 is about 100 times faster than the QC calculations. Thus, with ReaxFF we hope to be able to study complex reactions in hydrocarbons.

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and proteinligand, protein-protein, and protein-nucleic acid interactions.

A new real-time obstacle avoidance approach for mobile robots has been developed and implemented. This approach permits the detection of unknown obstacles simultaneously with the steering of the mobile robot to avoid collisions and advancing toward the target. The novelty of this approach, entitled the Virtual Force Field, lies in the integration of two known concepts: Cer- tainty Grids for

This article examines the extent to which there is congruence between the theorized world of tourism (the canon of tourism knowledge) and the phenomenal world of tourism. Adopting a social constructionist approach it conceptualizes and analyses the knowledge forcefield which is demonstrated to mediate between these two worlds. The five key factors that operate in the knowledge force-field are found to be person, rules, position, ends and ideology. The tourism literature is interrogated to demonstrate how these forces contribute to a doubleselectivity in knowledge creation. Despite many truths being established, the whole truth about tourism is left untold resulting in gaps, silences and mis-constructions.

A set of force field parameters is proposed for the molecular simulation of ionic liquids containing the anions trifluoromethylsufate and bis(trifluoromethylsulfonyl)imide, also known as triflate and bistriflylimide, respectively. The new set can be combined with existing force fields for cations in order to simulate common room-temperature ionic liquids, such as those of the dialkylimidazolium family, and can be integrated with the OPLS-AA or similar force fields. Ab initio quantum chemical calculations were employed to obtain molecular geometry, torsional energy profiles, and partial charge distribution in the triflate and bistriflylimide anions. One of the torsions in bistriflylimide, corresponding to the dihedral angle S-N-S-C, has a complex energy profile which is precisely reproduced by the present parameter set. A new set of partial electrostatic charges is also proposed for the pyrrolidinium and tri-and tetra-alkylammonium cations. Again, these parameters can be combined with the OPLS-AA specification for amines in order to simulate alkylammonium salts. The force-field models were validated against crystal structures and liquid-state densities.

Purpose -The purpose of this paper is to provide a holistic paradigmatic lens through which the supply chain collaboration phenomena -including collaborative inventory management -can be understood and explained. Design/methodology/approach -As theory-building research, the paper explores the environmental conditions and managerial processes that promote or hinder supply chain collaboration from a variety of theoretical lenses including contingency theory, the resource-based view of the firm, the relational view of the firm, force field analysis, constituency based theory, social dilemma theory, and resource-advantage theory. Findings -To demonstrate how an integrated theoretical framework can help us understand the dynamics of supply chain collaboration, the paper uses the framework to explicate the evolution and state of collaborative inventory management. Practical implications -The framework can accurately depict and explain highly publicized collaborative failures and successes. It is also possible to draw from the model's core propositions to design prescriptive remedies for the challenges managers encounter as they seek to build collaborative inventory management capabilities. Originality/value -Supply chain collaboration is a complex and dynamic phenomenon; however, existing management theories only describe locally observed phenomenon. As a result, it is a struggle to both explain existing "collaborative" behavior and provide prescriptions for leveraging collaboration to achieve differential supply chain performance. This holistic, integrative model delineates the path to collaborative success by exploring the connections among motivations, goals, mechanisms, resistors, and learning loops.

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of ϭ 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.

Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.

To predict the structures, properties, and chemistry of materials involving silicon and silicon oxides; interfaces between these materials; and hydrolysis of such systems, we have developed the ReaxFFSiO, reactive force field. The parameters for this force field were obtained from fitting to the results of quantum chemical (QC) calculations on the structures and energy barriers for a number of silicon

A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n e 6, the R crystal structure (with all-trans CH 2 chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, γ (with the alkane plane twisted by 70°) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young's modulus for nylon-7.

We extend the reactive force field ReaxFF to describe the high energy nitramine RDX and use it with molecular dynamics (MD) to study its shock-induced chemistry. We studied shock propagation via nonequilibrium MD simulations at various collision velocities. We find that for high impact velocities ( > 6 km=s) the RDX molecules decompose and react to form a variety of small molecules in very short time scales ( < 3 ps). These products are consistent with those found experimentally at longer times. For lower velocities only NO 2 is formed, also in agreement with experiments.

A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class I1 force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/ torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments.

Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS-AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas-phase structures and conformational energetics, experimental condensed-phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs.

This paper describes the design and analysis of hydraulic pallet system in a chain conveyor used in automobile industries for loading and unloading of materials .The system, consisting of a hydraulic power pack, a chain conveyor, a pallet system is automatically controlled with the help of PLC. Our aim is to design a feasible and a cost effective mechanism to lift the given load using hydraulic actuation and listing merits of hydraulic actuations over pneumatic and servo actuation. The design module pallet along with mechanism used for balancing is design in CAD software CATIA and analyzed for variable loading in ANSYS .The design proposed is highly flexible with the manufactures requirement and its stability is analyzed under variable load. The result of the feasibility study showed a conspicuous shortening of working hours, and an alleviation of manual labor.

The solid phase FT-IR and FT-Raman, solution phase linear dichroism IR (in nematic liquid crystal), and vapor phase GC/IR spectra of 2-(methylthio)benzonitrile have been recorded in the regions 4000–50, 3500–100, 4000–400, and 4000–650 cm−1, respectively. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimizations and force field calculations based on density functional theory (DFT) using standard B3LYP/6-31G* and B3LYP/6-311+G** method and basis set combinations. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. IR dichroism data revealed an error in band assignment associated with a νCS vibration, which could be eliminated only by introducing independent scaling factors for sulfur, whereas the overall frequency fit was further improved. Simulation of infrared and Raman spectra utilizing...

Six new 4-hydroxycoumarin derivatives have been synthesized. They were characterized by UV–vis, IR, 1H NMR, 13C NMR, mass spectral data, elemental analysis, TLC and melting point determination. The new 4-hydroxycoumarin derivatives are studied by computational methods – DFT (B3LYP) and force field methods (MM2 and OPLS), in order to optimize their geometry and calculate quantum-chemical properties and conformational analysis. Five

The pattern of occurrence of the massif-type anorthosites of the Proterozoic on a Rodinia reconstruction suggests that the geneses of the anorthosites, the associated granulites, and their chief repository-the Grenville age mobile belt may be interrelated. This relationship has been examined within the broad geodynamic and spatial-temporal framework of the Proterozoic supercontinent. All over the Grenville age mobile belt, approximately within 1500 -1000 Ma, two successive, back-to-back episodes can be recognized. A continent-continent collisional episode with massive sedimentation, great crustal shortening and thickening with large folds and nappes, metamorphism and calcalkaline magmatism, and accretion of juvenile crust was followed within little over a hundred million years or so by an extensional episode, beginning with large scale mantle-derived basic magma invasion, ponding and differentiation at the base of the thickened orogen, anorthosite diapirism and pervasive thermal overprinting of the lower and middle crust producing granulite belts. Cooling, unroofing and erosion of the orogen coincided with the later stages of the extension, which ended with splitting of the supercontinent. We have argued that the first episode marks the phase of closing in and amalgamation of the converging continental lithospheric plates and the second episode represents the phase of reversal, rifting, plate sepzration and drifting away of the post-split continental blocks. We believe, the supercontinental closing and opening cycles provide (a) realistic force fields and appropriate spatial-temporal and thermal-tectonic framework for the origin of the Proterozoic massif-type anorthosites and the associated granulites and (b) an explanation for the spatially overlapping but apparently conflicting evidence of both collisional and extensional tectonic signatures in the Grenvllle age orogenic belts.

Polymerehydroxyapatite (HAP) composites are widely studied as potential bone replacement materials. The HAPepolymer interfacial molecular interactions have significant role on the mechanical response of composite systems. We have used molecular dynamics (MD) simulations to evaluate the nature of these interfaces in polyacrylic acidehydroxyapatite composites. We have obtained the parameters for monoclinic hydroxyapatite in CVFF (consistent valence force field) from the known potential energy function of apatites. Our simulations indicate that potential sites for chelation and hydrogen bond formation between HAP and polyacrylic acid (PAAc) exist. Earlier, we have synthesized in situ HAPepolymer composites wherein intimate interaction between HAP and polymer is enabled through participation of polymer during HAP mineralization. Our simulations indicate that for in situ HAP, the most favorable orientation of PAAc for attachment with HAP is along the c-axis of HAP aligned parallel to polymer chains. Also, binding energy for ex situ HAP composites is found to be lower as compared to that of in situ HAP.

In Part−I, development and deployment of a general Nanoelectronic Modeling tool (NEMO 3-D) has been discussed. Based on the atomistic valence-force field (VFF) and the sp 3 d 5 s * nearest-neighbor tight-binding models, NEMO 3-D enables the computation of strain and electronic structure in nanostructures consisting of over 64 and 52 million atoms, corresponding to volumes of (110nm) 3 and (101nm) 3 , respectively. In this part, successful applications of NEMO 3-D are demonstrated in the atomistic calculation of single-particle electronic states of realistically-sized (1) self-assembled quantum dots (QDs) including long-range strain and piezoelectricity, (2) stacked quantum dot system as used in quantum cascade lasers, (3) SiGe quantum wells (QWs) for quantum computation, and (4) SiGe nanowires. These examples demostrate the broad NEMO 3-D capabilities and indicate the necessity of multimillion atomistic electronic structure modeling.

In the present study, a new method was developed to construct atomistic molecular models of crosslinked polymers based on commercially important epoxy resin. This method employed molecular dynamics/molecular mechanics schemes and assumed close proximity. The generic Dreiding2.21 force-field and advanced compass force-field were used for the construction of models and prediction of properties, respectively. A polymer network with conversion up to 93.7% was successfully generated by this method. Density and elastic constants of the system were calculated from the equilibrated structure for the validation of the generated models. The simulated results compared reasonably with experimental data available. The developed method would hold great promise in further molecular simulations for structure and properties of epoxy resin or other cured systems.

We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for R-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed.

This paper starts out by recalling the basic assumptions required for the classical (Cauchy type) continuum mechanics to hold. It turns out that the micro-and nano-scale structures of many materials -such as lattice-type porous solids and two-phase composites -may not satisfy the requirement of separation of scales and/or the postulate of negligible internal couple force fields. If that is the case, the mechanics of material cannot be predicted correctly by a classical theory of a Cauchy continuum. We give a sketch of history and achievements of non-classical (Cosserat type) elastic continua, and then focus on micropolar models, their planar cases, and the somewhat enigmatic characteristic lengths. This is followed by an outline of formulation of micropolar elasticity models for three beam-type lattices of classical geometries: triangular, square, and honeycomb. Next, we review very recent studies on determination of such models for two-phase (inclusion-matrix) periodic composites, which are locally of Cauchy type. It is shown that, in cases of both lattices and composites, the micropolar moduli and the characteristic lengths can be determined from first principles. The paper also provides a summary of the pros and cons of Cauchy vis-à-vis Cosserat models, and of the outstanding challenges in this field.

Objective: To carry out a proof of concept study for integrating robot therapy with physiotherapy in the treatment of stroke patients. Design: A simple and 'gentle' paradigm of robot-patient interaction was designed in order to foster the re-emergence of smooth, active control patterns in coordinated shoulder/elbow reaching movements. A haptic robot was programmed according to a strategy of minimal, progressively reduced assistance, with a double representation of targets: (i) visual (circles on a screen) and (ii) haptic (robot-generated force fields). The protocol included trials with and without vision, in order to emphasize the role of proprioceptive feedback. The training paradigm included 10 sessions and more than 5000 movements. Subjects: Ten chronic, hemiparetic subjects; four controls provided reference values for the performance measurements. Outcome measures: Four performance indicators (derived from the analysis of the reaching trajectories); clinical/functional measures (Fugl-Meyer and Ashworth scales). Results: After robot therapy reaching movements became faster and smoother. The performance in the no-vision trials was at least as good as in the vision trials. The Fugl-Meyer arm scores also increased significantly and remained approximately constant at follow-up; the Ashworth scores did not change. Conclusion: In spite of its simplicity, a limited number of 'gentle' robot therapy sessions appear to be beneficial, even for severely impaired patients, although no firm conclusion can be drawn at this point. However, the study provides support material for the careful design of controlled clinical trials and for a better integration with physiotherapy.

A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P-FQ potential. The proteins include 1FSV, 1ENH, 1PGB, 1VII, 1H8K, and 1CRN, representing both helical and ␤-sheet secondary structural elements. Constant pressure and temperature (NPT) molecular dynamics simulations are performed on time scales of several nanoseconds, the longest simulations yet reported using explicitly polarizable all-atom empirical potentials (for both solvent and protein) in the condensed phase. In terms of structure, the FQ force field allows deviations from native structure up to 2.5 Å (with a range of 1.0 to 2.5 Å). This is commensurate to the performance of the CHARMM22 nonpolarizable model and other currently existing polarizable models. Importantly, secondary structural elements maintain native structure in general to within 1 Å (both helix and ␤-strands), again in good agreement with the nonpolarizable case. In qualitative agreement with QM/MM ab initio dynamics on crambin (Liu et al. Proteins 2001, 44, 484), there is a sequence dependence of average condensed phase atomic charge for all proteins, a dependence one would anticipate considering the differing chemical environments around individual atoms; this is a subtle quantum mechanical feature captured in the FQ model but absent in current state-of-the-art nonpolarizable models. Furthermore, there is a mutual polarization of solvent and protein in the condensed phase. Solvent dipole moment distributions within the first and second solvation shells around the protein display a shift towards higher dipole moments (increases on the order of 0.2-0.3 Debye) relative to the bulk; protein polarization is manifested via the enhanced condensed phase charges of typical polar atoms such as backbone carbonyl oxygens, amide nitrogens, and amide hydrogens. Finally, to enlarge the sample set of proteins, gas-phase minimizations and 1 ps constant temperature simulations are performed on various-sized proteins to compare to earlier work by Kaminsky et al. (J Comp Chem 2002, 23, 1515). The present work establishes the feasibility of applying a fully polarizable force field for protein simulations and demonstrates the approach employed in extending the CHARMM force field to include these effects.

We present the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program [J. Mol. Biol. 168 (1983) 5951. Full details are given of the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution. Emphasis is placed on energy conservation and the nonbonded truncation schemes needed to achieve it. Simulations of macromolecules in solution with ENCAD are both very stable in that the native structure is preserved at room temperature and efficient in that nanosecond simulations take a few weeks on an ordinary workstation. 0 1995 Elsevier Science B.V. All rights reserved SSDI

We generalize the continuous time random walk (CTRW) to include the effect of space dependent jump probabilities. When the mean waiting time diverges we derive a fractional Fokker-Planck equation (FFPE). This equation describes anomalous diffusion in an external force field and close to thermal equilibrium. We discuss the domain of validity of the fractional kinetic equation. For the force free case we compare between the CTRW solution and that of the FFPE.

A specifically designed force-feedback device accurately simulated textures consisting of lateral forces opposing motion, simulating friction. The textures were either periodic trapezoidal forces, or sinusoidal forces spaced at various intervals from 1.5 mm to 8.5 mm. In each of two experiments, 10 subjects interacted with the virtual surfaces using the index finger placed on a mobile plate that produced the forces. The subjects selected their own speed and contact force for exploring the test surface. The apparatus returned force fields as a function of both the finger position and the force normal to the skin allowing full control over the tangential interaction force. In Experiment #1, subjects used an integer, numerical scale of their own choosing to rate the roughness of eight identical, varyingly spaced force ramps superimposed on a background resistance. The results indicated that subjective roughness was significantly, but negatively, correlated (mean r = -0.84) with the spatial period of the resistances for all subjects. In a second experiment, subjects evaluated the roughness of 80 different sinusoidal modulated force fields, which included 4 levels of resistance amplitude, 4 levels of baseline friction, and 5 spatial periods. Multiple regression was used to determine the relationship between friction, tangential force amplitude, and spatial period to roughness. Together, friction and tangential force amplitude produced a combined correlation of 0.70 with subjective roughness. The addition of spatial period only increased the multiple regression correlation to 0.71. The correlation between roughness estimates and the rate of change in tangential force was 0.72 in Experiment #1 and 0.57 in Experiment #2. The results suggest that the sensation of roughness is strongly influenced by friction and tangential force amplitude, whereas the spatial period of simulated texture alone makes a negligible contribution to the sensation of roughness.

A continuous¯ow microparticle ®lter that combines megahertz frequency ultrasonic standing waves and laminar¯ow is described. The ®lter has a 0.25 mm, single half wavelength, acoustic pathlength at right angles to the¯ow. Standing wave radiation pressure on suspended particles drives them towards the centre of the acoustic pathlength. Clari®ed suspending phase from the region closest to the ®lter wall is drawn away through a downstream outlet. Experimental tests achieved >1000-fold clearance of 5 mm yeast cells, at a sample¯ow rate of 6 ml min À1 , from which the clari®ed aliquot is 1 ml min À1 . At this¯ow rate the average residence time in the sound ®eld was <1 s. Latex particles of 25, 9, 5.7, 2.8 and 1.5 mm diameter were also tested. The temperature increase during an operating period >1 h was less than 1 K. The design criteria considered in the fabrication of this high performance device are discussed. A theoretical model of the ®lter's ef®ciency, which considers the action of primary radiation force and the particle distribution across a laminar¯ow pro®le is presented here. The model predicts that totally clari®ed ®ltrate (i.e. zero suspended particles) may be drawn from the downstream outlet. The system described offers a generic approach to automated ®ltration in some applications. It is continuous¯ow thereby solving many of the problems of automation presented by batch ®lter methods and centrifuges. It could be developed for both larger scale and micro¯uidic applications. # (J.J. Hawkes). 0925-4005/01/$ ± see front matter # 2001 Elsevier Science B.V. All rights reserved. PII: S 0 9 2 5 -4 0 0 5 ( 0 1 ) 0 0 5 5 3 -6

The communities organizing themselves for social change and the people working with them often face situations of conflicts. They need the ability to assess the situations well enough to find the possible alternatives and decide the future course of action. Often their efforts to change face resistance from different actors involved like employers, corporates, and governments. The change agents need to assess the situations completely, not in bits and pieces but in their wholeness, to see in advance such resistances they may encounter. Also, they need to recognize the right opportunity to initiate the process for change. Force Field Analysis (FFA) is a technique that helps with this complex task of reading the situation in its totality and understanding what can possibly be needed to change it. This paper contends that a well done FFA helps the change agents decide when and how to take an action, and also see when not to take any action. This paper seeks to bring a comprehensive understanding of the technique and illustrate its utility as well for the work of community organizing. The paper engages in theoretical discussion and then uses some case studies to illustrate the application of the technique.

The FFA technique is theoretically informed by field theory and systems theory. Field theory, developed by psychologist Kurt Lewin, explains how any situation is the result of all the different interacting and interdependent elements/actors that are concerned. The theory helps the change agents go beyond what is obvious to the eyes and get a macro-level perspective in order to understand and predict how change can happen, and if it is possible. Additionally, Lewin’s ideation of a field in its totality conceptually overlaps with the systems approach. All the actors concerning and capable of influencing a matter together form a system. Together these theoretical frameworks lay the foundation for FFA.

The paper also differentiates between FFA and other methods of situational assessment or risk assessment. The paper argues that the FFA informed by a systems approach is different from the usual situational analysis techniques. The technique gives such an overview of a system that explains the mutual relationships and positions of different actors involved, from a neutral perspective. The technique uncovers the complex interdependencies and interrelations of different actors/forces, which helps tremendously with strategizing future course of action.

Lastly, the paper explains the utility of FFA through Alinsky’s techniques of community organizing and mobilizing. Saul Alinsky, a formidable community organizer in US in the mid-twentieth century, often used means other than the obvious that surprised his unprepared opponents. Alinsky’s strength lay in his good analyses of existing situations and effective use of the potential forces for desired changes. Through the discussion of some of his works, the paper illustrates the practical application of FFA for community organizers.

Coal or biomass chars are complex carbonaceous materials that are important energy sources for electricity production. Reactive molecular dynamics simulations are a useful tool to examine the chemical reactions occurring in complex processes, providing that a realistic structural representation and an applicable reactive force field can be utilized. Combustion of coal (or biomass) char is one such area were additional insight would be helpful for utilization enhancements and pollution control. In this investigation a devolatilized Illinois No. 6 coal char atomistic representation was generated, using Fringe3D and additional Perl scripts, coupled with the ReaxFF reactive force field for hydrocarbon combustion. Fringe3D facilitates the char structure generation process by producing a distribution of aromatic structures based on HRTEM lattice fringe image analyses. Perl scripts were used for incorporating heteroatoms and aliphatic components to aid elimination of investigator bias, and facilitate a more rapid construction process. The char structure was constrained by a combination of elemental and NMR literature data. Chemical and physical parameters were found to be broadly consistent with the experimental data. The ReaxFF force field for hydrocarbon combustion was used to perform simulations to examine the structural transformations and chemical processes associated with char combustion. In this initial work, very high temperatures (3000-4000 K) were selected for ReaxFF simulation under stoichiometric, fuel lean and rich combustion conditions. These elevated temperatures were chosen to observe chemical reactions proceed to completion within a computationally practical simulation time. Analyses indicated that char oxidation process was primarily initialized by either thermal degradation of char structure to form small fragments, that were subsequently oxidized, or by hydrogen abstraction reactions by oxygen molecules and O and OH radicals. A more rapid oxidation and combustion of the polyaromatic structures occurred at fuel lean (oxygen rich) conditions compared with fuel rich combustion. Char transitions included 6-membered ring conversion into 5-and 7-membered rings that further decomposed or reacted with mostly O and OH radicals. This work further demonstrates the utility of ReaxFF force field integration with representative char structural models to investigate physical and chemical transformations of char structure during combustion at high-temperature conditions.

The response of cells to forces is essential for tissue morphogenesis and homeostasis. This response has been extensively investigated in interphase cells, but it remains unclear how forces affect dividing cells. We used a combination of micro-manipulation tools on human dividing cells to address the role of physical parameters of the micro-environment in controlling the cell division axis, a key element of tissue morphogenesis. We found that forces applied on the cell body direct spindle orientation during mitosis. We further show that external constraints induce a polarization of dynamic subcortical actin structures that correlate with spindle movements. We propose that cells divide according to cues provided by their mechanical micro-environment, aligning daughter cells with the external force field.

Une analyse ethnographique des politiques de titrement à Bangalore (Inde) éclaire quant aux contestations présentes des formes d'appropriation des territoires, lorsque les pratiques populaires sont confrontées à des élites convoquant de nouvelles options légales et institutionnelles, dont l'e-gouvernance, pour globaliser la ville. Nous mobilisons l'approche de Bourdieu et Wacquant, exprimée en termes de « champs de force », pour exposer deux aspects de ces jeux politiques : i) en quoi le sol, ses aspects matériels, sont ancrés dans un environnement émotionnel profond, et ii) en quoi ces dynamiques sont caractérisées par une fluidité politique façonnée par des alliances, mouvements et contre-mouvements entre groupes en compétitions. Les deux études de cas présentées ici invitent à considérer l'idée de politiques d'opacité. La représentation de telles politiques est nécessairement discontinue et amène à rejeter les récits cohérents et logiques des réformes foncières, qui dépolitisent pour justifier des modèles d'intervention bien définis.

There are a large number (N125) of molecular representations for coals that span the rank range over seven decades. However, their utility has mostly been in representing chemical structural features, rather than in probing physical structure or exploring the structure-behavior relationship. This paper examines the utility of coal models and reviews the existing and emerging opportunities for coal models to contribute to coals effective utilization via demystification of the structure-behavior relationship. Coal models have been used to explore the coalification pathway, including contraction with water removal. Physical evaluations have probed the density of models as a check on their accuracy. Pore size distribution and sorption have been explored in simple pores and more recent work with carbon dioxide, water and methane sorption within the porous structure of large-scale (b20,000 atoms) model. Pair distribution frequency and small angle X-ray scattering simulations have also been compared with experimental observations and offer an additional check on the constitution of the model structure. Simulated HRTEM and simulated (calculated) NMR spectra also exist. Models have been disassembled in efforts to represent the pyrolysis process, char formation, and char reactivity (including the role of ion-exchangable ions). Similar to the pyrolysis models, direct liquefaction has been explored with a pyrolysis style approach. Coal-solvent swelling, and coal-solvent solubility have also been explored. While considerable progress has accompanied improvements in computational power and software advances, it is the generation of the model that is the most significant barrier to the meaningful utility of these models. The ability to generate large-scale models (incorporation of molecular weight diversity and structural diversity) with new automation approaches, coupled with new dynamic force-fields that can simulate reactive events in complicated materials like coals, offers a new hope for the utility of coal or char molecular models to probe our understanding and aid in the scientific method rather than our current informed trial and error approach.

Discontinuities in the body force field typically appear at the interface of two fluid systems. Modeled with the volumeof-fluid (VOF) and discretized with the finite volume method, the discontinuous body force fields are represented as abruptly variable. In the present study, gravity and continuum surface force (CSF) are considered. Such strongly variable body forces can produce unphysical spikes in the velocity field when collocated variable arrangement is used. The spikes can be eliminated following a force field discretization rule which is deduced by imposing a constraint requiring a zero velocity solution when the forces applied to the system are equilibrated with the gradient of the pressure field. It is shown (as a byproduct of the present work) that a zero velocity solution can only be obtained if the force field is conservative on the discrete level, which applies also for the studied case of a stationary bubble. Finally, the case of a rising bubble demonstrates that the proposed rule should be obeyed generally although it is obtained for a quiescent fluid.

13-cis-Retinoic acid (13-cis-RA) is a synthetic retinoid commonly used in the treatment of severe acne. It has also been found to possess potential chemopreventive activity. It has extremely low aqueous solubility and high photo-sensitivity. This study investigated the effects of the complexation of 13-cis-RA with ␣-cyclodextrin (␣-CD) and hydroxypropyl-␤-cyclodextrin (HP-␤-CD) on its phase solubility. HP-␤-CD was found to be more effective in increasing the aqueous solubility of 13-cis-RA compared to ␣-CD. Phase solubility studies indicated that the solubility of 13-cis-RA was increased dramatically by the formation of inclusion complex with HP-␤-CD. The solubility was further enhanced by pH adjustment. The photostability of the selected inclusion complex of 13-cis-RA:HP-␤-CD was then evaluated. Complexation with HP-␤-CD was found to delay the photo-degradation of 13-cis-RA in aqueous solution. The physicochemical properties of the solid inclusion complex were characterized by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and X-ray diffractometry (XRD). Molecular modeling with MMFF94s force field (SYBYL V6.6) was utilized to predict the preferred orientation of 13-cis-RA in the CD cavity and the main structural features responsible for the enhancement of its solubility and photostability. The energy scores estimated from the computational analysis were found capable of reflecting the stability constants of the cyclodextrin complexes obtained in the phase solubility studies. The results showed that HP-␤-CD was a proper excipient for increasing solubility and stability of 13-cis-RA.

We propose a scheme for quantum Brownian motion of a particle in a fermionic bath. Based on the spin coherent-state representation of the noise operators and a canonical thermal distribution of the associated c numbers, we derive a quantum analog of generalized Langevin equation for quantum-mechanical mean position of the particle subjected to an external force field. The approach allows us to map the quantum problem on a classical setting. The quantum dispersion around the mean can be estimated order by order by a set of quantum correction equations up to a desired degree of accuracy for a given nonlinear potential. We derive a quantum diffusion equation for free particle and show that quantization, in general, enhances the mean-square displacement. Increase in temperature leads to suppression of mean-square displacement. The method is based on canonical quantization procedure and may be used for understanding diffusive transport and thermally activated processes in a fermionic bath.

The adhesion of TiO 2 (anatase structure) nanoparticles to kaolinite substrate was investigated using molecular modeling. Universal force field computation, density function theory computation, and a combination of both two approaches were used. This study enabled the adhesion energy for the TiO 2 /kaolinite nanocomposite to be estimated, and revealed the preferred orientation of the TiO 2 nanoparticles on the kaolinite substrate. The results of all three levels of computation were compared in order to show that the accuracy of universal force field computations is sufficient in this context. The role of nanoparticle size and the importance of the nanoparticle-substrate bonding contribution are presented here and discussed. A comparison of the molecular modeling results with scanning electron microscopy observations showed that the results of the modeling were consistent with the experimental data, and that this approach can be used to help characterize nanocomposites of the nanoparticle/phyllosilicate substrate type.

The capabilities and limitations of the application of molecular simulation techniques to the adsorption of hydrogen in metal-organic frameworks (MOFs) are explored for selected case studies. Force field based grand-canonical Monte Carlo simulations are employed to investigate the adsorption characteristics of three different isoreticular MOFs, resulting in good agreement with experimental findings. The predictive potential of the method is demonstrated for Zn 4 O(mip) 3 , a novel system which has not yet been fully characterized experimentally. Further calculations for MOFs with unsaturated metal sites reveal a shortcoming of the simulation technique, as the interaction of hydrogen with these sites is not adequately represented by the potential model. Density functional theory calculations are employed to study the metal-dihydrogen interaction in more detail, making use of a non-periodic model system which is representative for many copper-containing MOFs.

Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligandprotein systems by a combined thermodynamic and kinetic analysis of the binding energy landscapes. Misdocked predictions in ligand-protein docking are classified as 'soft' and 'hard' failures. While a soft failure arises when the search algorithm is unable to find the global energy minimum corresponding to the crystal structure, a hard failure results from a flaw of the energy function to qualify the crystal structure as the predicted lowest energy conformation in docking simulations. We find that neither the determination of a single structure with the lowest energy nor finding the most common binding mode is sufficient to predict crystal structures of the complexes, which belong to the category of hard failures. In a proposed hierarchical approach, structural similarity clustering of the conformations, generated from equilibrium simulations with the simplified energy function, is followed by energy refinement with the AMBER force field. This protocol, that involves a hierarchy of energy functions, resolves some common failures in ligand-protein docking and detects crystallographic binding modes that were not found during docking simulations.

at 3:04 a.m., an earthquake of 7.4 magnitude (Richter scale) struck the Marmara region in Turkey. The city of Adapazari suffered 2,680 fatalities with approximately 5,300 injured. The Israeli Defence Forces (IDF) field hospital arrived at Adapazari, on day four after the quake. The team consisted of 102 personnel. The field hospital acted as a secondary referral centre. A total of 1,205 patients were treated in the field hospital between day four and day 14 of the earthquake. The frequency distribution of the medical problems seen in the field hospital was 32 per cent internal medicine, 13 per cent general surgery including plastic, 21 per cent orthopaedic surgery, 23 per cent paediatric disease, 10 per cent obstetrics and gynaecology and 1 per cent major psychiatric disorders. A mean number of 35 patients per day were hospitalised in the field hospital for between 24 hours to one week. Israeli Defence Force Field Hospital in the Turkish Earthquake 263

Interest in microporous materials has risen in recent years, as they offer a confined environment that is optimal to enhance chemical reactions. Calcium silicate hydrate (C-S-H) gel, the main component of cement, presents a layered structure with sub-nanometer-size disordered pores filled with water and cations. The size of the pores and the hydrophilicity of the environment make C-S-H gel an excellent system to study the possibility of confined water reactions. To investigate it, we have performed molecular dynamics simulations using the ReaxFF force field. The results show that water does dissociate to form hydroxyl groups. We have analyzed the water dissociation mechanism, as well as the changes in the structure and water affinity of the C-S-H matrix and water polarization, comparing the results with the behavior of water in a defective zeolite. Finally, we establish a relationship between water dissociation in C-S-H gel and the increase of hardness due to a transformation from a two-to a three-dimensional structure.

Molecular dynamics simulations are used to study the dynamics and transport properties of 12 room-temperature ionic liquids of the 1-alkyl-3-methylimidazolium ͓amim͔ + ͑alkyl= methyl, ethyl, propyl, and butyl͒ family with PF 6 − , NO 3 − , and Cl − counterions. The explicit atom transferable force field of Canongia Lopes et al. ͓J. Phys. Chem. B 108, 2038 ͑2004͔͒ is used in the simulations. In this first part, the dynamics of the ionic liquids are characterized by studying the mean-square displacement ͑MSD͒ and the velocity autocorrelation function ͑VACF͒ for the centers of mass of the ions at 400 K. Trajectory averaging was employed to evaluate the diffusion coefficients at two temperatures from the linear slope of MSD͑t͒ functions in the range of 150-300 ps and from the integration of the VACF͑t͒ functions at 400 K. Detailed comparisons are made between the diffusion results from the MSD and VACF methods. The diffusion coefficients from the integration of the VACFs are closer to experimental values than the diffusion coefficients calculated from the slope of MSDs. Both methods can show good agreement with experiment in predicting relative trends in the diffusion coefficients and determining the role of the cation and anion structures on the dynamical behavior of this family of ionic liquids. The MSD and self-diffusion of relatively heavier imidazolium cations are larger than those of the lighter anions from the Einstein results, except for the case of ͓bmim͔͓Cl͔. The cationic transference number generally decreases with temperature, in good agreement with experiments. For the same anion, the cationic transference numbers decrease with increasing length of the alkyl chain, and for the same cation, the trends in the cationic transference numbers are ͓NO 3 ͔ − Ͻ ͓Cl͔ − Ͻ ͓PF 6 ͔ − . The trends in the diffusion coefficient in the series of cations with identical anions are ͓emim͔ + Ͼ ͓pmim͔ + Ͼ ͓bmim͔ + and those for anions with identical cations are ͓NO 3 ͔ − Ͼ ͓PF 6 ͔ − Ͼ ͓Cl͔ − . The ͓dmim͔ + has a relatively low diffusion coefficient due to its symmetric structure and good packing in the liquid phase. The major factor for determining the magnitude of the self-diffusion is the geometric shape of the anion of the ionic liquid. Other important factors are the ion size and the charge delocalization in the anion.

Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling. From the Contents 1. Introduction 4065 2. The Force-Field Problem 4067 3. The Search Problem 4073 4. The Ensemble Problem 4080 5. The Experimental Problem 4083 6. Perspectives in Biomolecular Modeling 4087 Biomolecular Modeling Angewandte Chemie Boundary conditions MOLECULAR MODEL Degrees of freedom: atoms are the elementary particles Forces or interactions between atoms Methods to generate configurations of atoms: Newton system temperature pressure walls external forces Force field = physicochemical knowledge