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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…
Thermally bistable fluid tends to self-organize into clouds of hot and cold material, which are internally uniform and separated by thin conduction fronts. The evolution of these clouds has been studied for isobaric systems, but when…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
We show a unified second-order scheme for constructing simple, robust and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB…
Quantitative Systems Pharmacology (QSP) promises to accelerate drug development, enable personalized medicine, and improve the predictability of clinical outcomes. Realizing this potential requires effectively managing the complexity of…
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…
Developing enzymes with desired thermal properties is crucial for a wide range of industrial and research applications, and determining temperature stability is an essential step in this process. Experimental determination of thermal…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable),…
Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…
We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev.…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
The cosmic microwave background (CMB) temperature anisotropies exhibit a large-scale dipolar power asymmetry. To determine whether this is due to a real, physical modulation or is simply a large statistical fluctuation requires the…
We use molecular dynamics to study the vibrations of a thermally fluctuating two-dimensional elastic membrane clamped at both ends. We directly extract the eigenmodes from resonant peaks in the frequency domain of the time-dependent height…
A set formed by five reversibly-switchable fluorescent proteins (RSFPs) display spread over 40~nm in absorption maxima and only 18~nm in emission. The five proteins -- Dronpa, rsFastLime, rsKame, Padron(anionic form) and bsDronpa -- carry…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Literature and experimental data about practical determination of phase composition and structure of BiHTSC ceramics from results of measurements of temperature dependence of magnetic susceptibility are presented. It is shown that Bi2223 to…
The use of excessively long timesteps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational…
We report the first experimental observation of dissipation-driven coherent quantum many-body oscillation, and this oscillation is manifested as the coherent exchange of atoms between the thermal and the condensate components in a…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
The transfer of weakly bound KRb molecules from levels just below the dissociation threshold into the vibrational ground state with shaped laser pulses is studied. Optimal control theory is employed to calculate the pulses. The complexity…