相关论文: Multi-Overlap Simulations for Transitions between …
We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space…
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting…
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential.…
We apply the minimum energy paths (MEPs) approach to study the helix unwinding transition in chiral nematic liquid crystals. A mechanism of the transition is determined by a MEP passing through a first order saddle point on the free energy…
Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and…
The multicanonical ansatz is used to study variations in the energy landscape of a small peptide, Met-enkephalin, under a change from the ECEPP/2 force field to ECEPP/3. Local minima with energies up to 5 kcal/mol higher than the global…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
Humans effortlessly navigate the physical world by predicting how objects behave under gravity and contact forces, yet how such judgments support sequential physical planning under resource constraints remains poorly understood. Research on…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
Met-enkephalin, one of the smallest opiate peptides and an important neurotransmitter, is a widely used benchmarking problem in the field of molecular simulation. Through its range of possible low-temperature conformations separated by…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
We study a three-dimensional plaquette spin model whose low temperature dynamics is glassy, due to localised defects and effective kinetic constraints. While the thermodynamics of this system is smooth at all temperatures, we show that…
We establish a renormalization group approach which is implemented on the degrees of freedom defined by the overlap of two replicas to determine the critical fixed point and to extract four critical exponents for the phase transition of the…
A set of density functionals coming from different rungs on Jacob's ladder are employed to evaluate the electronic excited states of three Ru(II) complexes. While most studies on the performance of density functionals compare the vertical…