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The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
Controlled quantum systems such as ultracold atoms can provide powerful platforms to study non-equilibrium dynamics of closed many-body quantum systems, especially since a complete theoretical description is generally challenging. In this…
We present an embedding technique for metallic systems that makes it possible to model energy dissipation into substrate phonons during surface chemical reactions from first principles. The separation of chemical and elastic contributions…
Understanding interactions between membranes requires measurements on well-controlled systems close to natural conditions, in which fluctuations play an important role. We have determined, by grazing incidence X-ray scattering, the…
Multiscale modeling and analysis of multiphysics coupling processes in highly heterogeneous media present significant challenges. In this paper, we propose a novel multiphysics embedding localized orthogonal decomposition (ME-LOD) method…
We propose a general framework to study transformations that drive an underdamped Brownian particle in contact with a thermal bath from an equilibrium state to a new one in an arbitrarily short time. To this end, we make use of a time and…
We consider the evolution of interfaces in binary mixtures permeating strongly heterogeneous systems such as porous media. To this end, we first review available thermodynamic formulations for binary mixtures based on \emph{general…
We study the one-dimensional hard-core Bose-Hubbard model with three-body interactions. In previous work[1], the two-thirds filling solid with both bond-wave order (BOW) and charge-density wave order (CDW) is found and it undergoes a second…
We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228),…
Microscopic thermodynamic studies can elucidate specific molecular interactions. In this work, we report the microscopic thermodynamics in binary liquid mixtures, which elucidate the role of molecular structure in nonlinear solvent response…
Twenty years ago Poole et al. (Nature 360, 324, 1992) suggested that the anomalous properties of supercooled water may be caused by a critical point that terminates a line of liquid-liquid separation of lower-density and higher-density…
Liquid-liquid phase transition (LLPT) in supercooled water has been a long-standing controversial issue. We show simulation results of real stable first-order phase transitions between high and low density liquid (HDL and LDL)-like…
We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray…
We introduce an effective thermodynamics for multipartite entangled pure states and derive an upper bound on extractable energy with feedback control from a subsystem under a local Hamiltonian. The inequality that gives the upper bound…
We investigate the thermodynamics and transient dynamics of the (unbiased) Ohmic two-state system by exploiting the equivalence of this model to the interacting resonant level model. For the thermodynamics, we show, by using the numerical…
We consider the problem of finding the energy minimum of a complex quantum Hamiltonian by employing a non-Markovian bath prepared in a low energy state. The energy minimization problem is thus turned into a thermodynamic cooling protocol in…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
The thermodynamics of hydration changes gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as…