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Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…
Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a million particles were conducted with a massively parallel MD…
Leukemia epitomizes the class of highly complex diseases that new technologies aim to tackle by using large sets of single-cell level information. Achieving such goal depends critically not only on experimental techniques but also on…
One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here I derive equations for the equilibrium distributions generated by…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Short-timescale atomic rearrangements are fundamental to the kinetics of glasses and frequently dominated by one atom moving significantly (a rearrangement), while others relax only modestly. The rates and directions of such rearrangements…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
We study a continuum model of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules. This paper extends previous work by Blom & Peletier (2004) in the following ways. (a) It formulates a more…
Metaheuristics, as the simulated annealing used in the optimization of disordered systems, goes beyond physics, and the traveling salesman is a paradigmatic NP-complete problem that allows inferring important theoretical properties of the…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
The combination of the catechol-containing co-monomer dopamine methacrylamide (DMA) with stimuli-responsive microgels such as poly(N-isopropylacrylamide) (PNIPAM) bears a huge potential in research and for applications due to the versatile…
There are well developed theoretical tools to analyse how quantum dynamics can solve computational problems by varying Hamiltonian parameters slowly, near the adiabatic limit. On the other hand, there are relatively few tools to understand…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
This letter highlights the entropy exchange phenomenon in a coupled binary inter-correlating system following Haldane's non-linear statistical correlation. A unique coupling between a classical and a quantum-like system at the marginal…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…