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Journal of Chemical Theory and Computation

Patrick Shaffer, Omar Valsson, Michele Parrinello
In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate...
November 4, 2016: Journal of Chemical Theory and Computation
Jerelle Aurelia Joseph, Chris S Whittleston, David J Wales
We investigate how the underlying potential energy landscape for a tryptophan zipper changes as indole rings, peptide bonds, termini and trigonal planar centers are systematically grouped into local rigid bodies. The local rigid body framework results in a substantial computational speedup by effectively reducing the total number of degrees of freedom. Benchmarks are presented for the thermodynamics and folding mechanism. In general, the melting transition, as well as the precise sequence of folding events, is accurately reproduced with conservative local rigidification...
November 3, 2016: Journal of Chemical Theory and Computation
Silvio Osella, Natarajan Arul Murugan, Naresh Kumar Jena, Stefan Knippenberg
The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid head-group region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group towards the head of the membrane, with an angle of 50° between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan head-group whose carbonyl group is oriented towards the polar regions of the membrane and which describes an angle of ca...
November 2, 2016: Journal of Chemical Theory and Computation
Ryan L Melvin, Ryan C Godwin, Jiajie Xiao, William G Thompson, Kenneth S Berenhaut, Freddie R Salsbury
As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majority require users to either have some \textit{a priori} knowledge about the system to be clustered or to tune clustering parameters through trial and error. Here we present non-parametric uses of two modern clustering techniques suitable for first-pass investigation of an MD trajectory...
November 1, 2016: Journal of Chemical Theory and Computation
Zhongwei Hu, Dhabih V Chulhai, Lasse Jensen
Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule...
October 28, 2016: Journal of Chemical Theory and Computation
Guillermo Pérez-Hérnandez, Frank Noé
Analysis of molecular dynamics, for example using Markov models, often require the identification of order parameters that are good indicators of the rare events, i.e. good reaction coordinates. Recently, it has been shown that the time-lagged independent component analysis (TICA) finds the linear combinations of input coordinates that optimally represent the slow kinetic modes and may serve in order to define reaction coordinates between the metastable states of the molecular system. A limitation of the method is that both computing time and memory requirements scale with the square of the number of input features...
October 28, 2016: Journal of Chemical Theory and Computation
Lukas Konecny, Marius Kadek, Stanislav Komorovsky, Olga L Malkina, Kenneth Ruud, Michal Repisky
The Liouville-von Neumann equation based on the four-component matrix Dirac-Kohn-Sham Hamiltonian is transformed to a quasirelativistic exact two-component (X2C) form, and then used to solve the time evolution of the electronic states only. By this means, a significant acceleration by a factor of seven or more has been achieved. The transformation of the original four-component equation of motion is formulated entirely in matrix algebra, following closely the X2C decoupling procedure of Ilias and Saue [J. Chem...
October 28, 2016: Journal of Chemical Theory and Computation
Pavel Janoš, Tomáš Trnka, Stanislav Kozmon, Igor Tvaroska, Jaroslav Koča
Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that can be exploited for rational drug design. Various approaches are available for such studies. However, their strengths and weaknesses may not be immediately apparent. Using the retaining glycosyltransferase ppGalNAcT2 as a case study, we compare different methodologies used to obtain reaction paths and transition state information. Ab Initio MD using CPMD coupled with String Method is used to derive the minimum free energy reaction path...
October 27, 2016: Journal of Chemical Theory and Computation
Keri A McKiernan, Lee-Ping Wang, Vijay S Pande
We present an united-atom model (gb-fb15) for the molecular dynamics simulation of hydrated liquid-crystalline dipalmitoylphosphatidylcholine (DPPC) phospholipid bilayers. This model was constructed through the parameter-space minimization of a regularized least squares objective function via the ForceBalance method. The objective function was computed using a training set of experimental bilayer area per lipid and deuterium order parameter. This model was validated by comparison to experimental volume per lipid, x-ray scattering form factor, thermal area expansivity, area compressibility modulus and lipid lateral diffusion coefficient...
October 27, 2016: Journal of Chemical Theory and Computation
Anastasia Kruchinina, Elias Rudberg, Emanuel H Rubensson
Parameterless stopping criteria for recursive polynomial expansions to construct the density matrix in electronic structure calculations are proposed. Based on convergence order estimation the new stopping criteria automatically and accurately detect when the calculation is dominated by numerical errors and continued iteration does not improve the result. Difficulties in selecting a stopping tolerance and appropriately balancing it in relation to parameters controlling the numerical accuracy are avoided. Thus, our parameterless stopping criteria stand in contrast to the standard approach to stop as soon as some error measure goes below a user-defined parameter or tolerance...
October 26, 2016: Journal of Chemical Theory and Computation
Cannada Andrew Lewis, Justus Aaron Calvin, Edward F Valeev
We describe the Clustered Low Rank (CLR) framework for block-sparse and block-low-rank tensor representation and computation. The CLR framework exploits the tensor structure revealed by basis clustering; computational savings arise from low-rank compression of tensor blocks and performing block arithmetic in the low-rank form whenever beneficial. The precision is rigorously controlled by 2 parameters, avoiding ad-hoc heuristics, such as domains: one controls the CLR block rank truncation and the other controls screening of small contributions in arithmetic operations on CLR tensors to propagate sparsity through expressions...
October 26, 2016: Journal of Chemical Theory and Computation
Min Li, Fengjiao Liu, John Zenghui Zhang
Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system, and thus provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems...
October 26, 2016: Journal of Chemical Theory and Computation
Jan Wilhelm, Patrick Seewald, Mauro Del Ben, Juerg Hutter
We present an algorithm for computing the correlation energy in the random phase approximation (RPA) in a Gaussian basis requiring $\mathcal{O}(N^3)$ operations and $\mathcal{O}(N^2)$ memory. The method is based on the resolution of the identity (RI) with the overlap metric, a reformulation of RI-RPA in the Gaussian basis, imaginary time and imaginary frequency integration techniques and the use of sparse linear algebra. Additional memory reduction without extra computations can be achieved by an iterative scheme which overcomes the memory bottleneck of canonical RPA implementations...
October 25, 2016: Journal of Chemical Theory and Computation
Daniel Ricardo Nascimento, A Eugene DePrince
We report an explicitly time-dependent approach to the generation of linear absorption spectra for molecular systems within the framework of equation-of-motion (EOM) coupled-cluster (CC) theory. While most time-dependent CC approaches consider the perturbation and time-evolution of a CC wave function, the present work considers the time-evolution of a CC dipole function. The dipole function formalism introduces no approximations and requires the evolution of only one time-dependent quantity, either the left or the right dipole function...
October 25, 2016: Journal of Chemical Theory and Computation
John F Ouyang, Ryan P A Bettens
Many-body effects are required for an accurate description of both structure and dynamics of large chemical systems. However, there are numerous such interactions to consider and it is not obvious which ones are significant. We provide a general and fast method for establishing which small set of three- and four-body interactions are important. This is achieved by estimating the maximum many-body effects, $\epsilon_\mathrm{max}$, that can arise in a given arrangement of bodies. Through careful analysis of $\epsilon_\mathrm{max}$ we find two overall causes for significant many-body interactions...
October 25, 2016: Journal of Chemical Theory and Computation
Federico Melaccio, María Del Carmen Marín, Alessio Valentini, Fabio Montisci, Silvia Rinaldi, Marco Cherubini, Xuchun Yang, Yoshitaka Kato, Michael Stenrup, Yoelvis Orozco-Gonzalez, Nicolas Ferré, Hoi Ling Luk, Hideki Kandori, Massimo Olivucci
We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side-chains and distributions of external counterions. Starting with such information a model formed by a fixed environment system, a flexible cavity system and a chromophore system is automatically generated...
October 25, 2016: Journal of Chemical Theory and Computation
Karen Druart, Julien Bigot, Edouard Audit, Thomas Simonson
Multistate protein design explores sidechain mutations with the backbone allowed to sample a small, predetermined library of conformations. To achieve Boltzmann sampling of sequences and conformations, we use a hybrid Monte Carlo (MC) scheme: a trial hop between backbone models is followed by a short MC segment where sidechain rotamers adjust to the new backbone, before applying a Metropolis-like acceptance test. The theoretical form and a practical approximation for the acceptance test are derived. We then compute backbone conformational free energies for two SH2 and SH3 proteins using different routes and protocols, and verify that for simple test problems, the free energy behaves like a state function, a hallmark of Boltzmann sampling...
October 24, 2016: Journal of Chemical Theory and Computation
Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Nathan A Bernhardt, Wenhui Xi, Wei Wang, Ulrich H E Hansmann
Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms essential for its function, or important during folding or association. These various forms populate a multi-funnel folding and association landscape where mutations, changes in environment or interaction with other molecules switch between the encoded folds. We introduce replica-exchange-with- tunneling as a way to simulate efficiently switching between distinct folds of proteins and protein aggregates...
October 21, 2016: Journal of Chemical Theory and Computation
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