相关论文: Thermodynamic relations at the coupling boundary i…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the…
We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems,…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
openCOSMO-RS is an open-source predictive thermodynamic model that can be applied to a broad range of systems in various chemical and biochemical engineering domains. This study focuses on improving openCOSMO-RS by introducing a new…
Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…
A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct…
We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution…
In this paper, we study a sequential decision-making problem, called Adaptive Sampling for Discovery (ASD). Starting with a large unlabeled dataset, algorithms for ASD adaptively label the points with the goal to maximize the sum of…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to…
We consider growing open chemical reaction systems (CRSs), in which autocatalytic chemical reactions are encapsulated in a finite volume and its size can change in conjunction with the reactions. The thermodynamics of growing CRSs is…
Our primary goal in this paper is to confirm new universal relations in black hole thermodynamics. We investigate the universal relations by selecting different black holes. First, we obtain the black holes' thermodynamic relations assuming…
The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved…
We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
With the development of 3D modelling techniques and AR techniques, the traditional methods of establishing 2D to 3D relation is no longer sufficient to meet the demand for complex models and rapid relation building. This dissertation…