Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc.     

原子力显微镜在蛋白单分子结构与功能研究中的应用

原子力显微镜(AFM)以其超常的信噪比、空间分辨率和灵活的探测环境使得单个蛋白分子能在生理条件下成像,在蛋白单分子结构与功能研究中得到广泛地应用。论文介绍了AFM在分子马达、光合蛋白、分子伴侣等蛋白表面结构表征中的应用;AFM在蛋白单分子表面的粘弹性、电荷分布、分子间相互作用等物理属性研究中的进展;总结了AFM在蛋白分子功能研究和单分子操纵中的应用。     

Computer simulation studies on the interactions between nanoparticles and cell membrane

In recent times,nanoparticles(NPs)have received intense attention not only due to their potential applications as a candidate for drug delivery,but also because of their undesirable effects on human health.Although extensive experimental studies have been carried out in literature in order to understand the interaction between NPs and a plasma membrane,much less is known about the molecular details of the interaction mechanisms and pathways.As complimentary tools,coarse grained molecular dynamics(CGMD)and dissipative particle dynamics(DPD)simulations have been extensively used on the interaction mechanism and evolution pathway.In the present review we summarize computer simulation studies on the NP-membrane interaction,which developed over the last few years,and particularly evaluate the results from the DPD technique.Those studies undoubtedly deepen our understanding of the NP-membrane interaction mechanisms and provide a design guideline for new NPs.     

ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions

In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines state-of-the-art molecular dynamics (MD) algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, reversible reference system propagation algorithm) specifically designed and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps of standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1848–1862, 1997     

Motion Capture and Manipulation of a Single Synthetic Molecular Rotor by Optical Microscopy

Single‐molecule imaging and manipulation with optical microscopy have become essential methods for studying biomolecular machines; however, only few efforts have been directed towards synthetic molecular machines. Single‐molecule optical microscopy was now applied to a synthetic molecular rotor, a double‐decker porphyrin (DD). By attaching a magnetic bead (ca. 200 nm) to the DD, its rotational dynamics were captured with a time resolution of 0.5 ms. DD showed rotational diffusion with 90° steps, which is consistent with its four‐fold structural symmetry. Kinetic analysis revealed the first‐order kinetics of the 90° step with a rate constant of 2.8 s^?1. The barrier height of the rotational potential was estimated to be greater than 7.4 kJ mol^?1 at 298 K. The DD was also forcibly rotated with magnetic tweezers, and again, four stable pausing angles that are separated by 90° were observed. These results demonstrate the potency of single‐molecule optical microscopy for the elucidation of elementary properties of synthetic molecular machines.     

Molecular dynamics study of polymer crystallization in the presence of a particle

We have used molecular dynamics simulations with a coarse‐grained model to study the effect of a particle on the crystallization of polymer melt. We analyzed in particular a bond order parameter to characterize the nucleation and crystallization process. Our calculations show that the presence of a particle modifies the free energy landscape of polymer melts, locally induces the ordering of polymer melts near the particle surface, and thus enhances the polymer crystallization. Because the interaction between the particle and polymers is repulsive, our results suggest that the origin of the enhancement for polymer crystallization is entropic. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2161–2166, 2007     

Photodissociation study of ethyl bromide in the ultraviolet range by the ion-velocity imaging technique.

The photodissociation of ethyl bromide has been studied in the wavelength range of 231-267 nm by means of the ion velocity imaging technique coupled with a [2+1] resonance-enhanced multiphoton ionization (REMPI) scheme. The velocity distributions for the Br ((2)P(1/2)) (denoted Br*) and Br ((2)P(3/2)) (denoted Br) fragments are determined, and each can be well-fitted by a narrow single-peaked Gaussian curve, which suggests that the bromine fragments are generated as a result of direct dissociation via repulsive potential-energy surfaces (PES). The recoil anisotropy results show that beta(Br) and beta(Br*) decrease with the wavelength, and the angular distributions of Br* suggest a typical parallel transition. The product relative quantum yields at two different wavelengths are Phi(234nm)(Br*)=0.17 and Phi(267nm)(Br*)=0.31. The relative fractions of each potential surface for the bromine fragments' production at 234 and 267 nm reveal the existence of a curve crossing between the (3)Q(0) and (1)Q(1) potential surfaces, and the probability of curve crossing decreases with the laser wavelength. The symmetry reduction of C(2)H(5)Br from C(3v) to C(s) invokes a nonadiabatic coupling between the (3)Q(0) and (1)Q(1) states, and with higher energy photons, the probability that crossing will take place increases.     

聚合物与表面活性剂相互作用的分子模拟研究进展

聚合物与表面活性剂复配体系已广泛应用于医药、生物、石油石化等领域。从微观上认识其相互作用机理对指导其生产实际有着重要作用,因而此方面的研究倍受关注。随着分子模拟技术的发展,聚合物与表面活性剂在分子水平上的相互作用机理研究已经被广泛开展,并获得了大量有用的信息。本文综述了耗散粒子动力学(DPD)和粗粒度分子动力学(CG-MD)在聚合物与表面活性剂相互作用方面的应用,分别对中性聚合物与离子型表面活性剂,以及带相反电荷的聚电解质和表面活性剂在溶液相和界面相的相互作用进行了阐述,并揭示了聚合物/表面活性剂聚集体结构形态的变化规律。     

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions

Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R(3/2)p(-1/2)), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice.