12 papers · ranked by Valyu relevance
Zhenghao Wu, Tianhang Zhou
In the realm of multiscale molecular simulations, structure-based coarse graining is a prominent approach for creating efficient coarse-grained (CG) representations of soft matter systems such as polymers. This involves optimizing CG interactions by matching static correlation functions of corresponding degrees of…
Benedikt Axel Brandes
In this contribution, I derive the transition state theory through a probabilistic model embedded in statistical mechanics. This leads to a formulation equivalent to the Eyring equation proving that the transfer coefficient must always be one. This derivation proves that the transition between two systems that are…
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We developed OpenStats, a user-friendly web application that brings the power of the R language to researchers through a high-level interface and broad support for statistical methods such as t-tests and ANOVA. OpenStats was integrated into our electronic lab notebook Chemotion ELN via its third-party API, enabling…
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This paper introduces simple phenomenological rate theory from the perspective of molecular interconversions and then applies it, in the form of Transition State Theory, to processes such as atomic diffusion and thermally-activated crystal growth in condensed matter composed of very large numbers of atoms or molecules.…
Sara Giarrusso, Paola Gori-Giorgi, Federica Agostini
We generalize the definitions of local scalar potentials named vkin and vN−1, which are relevant to properly describe phenomena such as molecular dissociation with density-functional theory, to the case in which the electronic wavefunction corresponds to a complex current-carrying state. In such a case, an extra term…
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The rapid growth of worldwide computing power has transformed in silico chemistry into a discipline that is integrated into the daily work of many chemists. Nowadays, researchers find it increasingly straightforward to predict a wide range of molecular properties and chemi- cal processes at reasonable computational…
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Relation between triple point temperature and the Rydberg constant based on the semi-phenomenological approach is found. To explain squared number 17 set in factor of proportionality, we use the Poisson distribution to be valid for some groups of thermal vibrations in pure water. We formulate a theorem explaining…
Brittany Story, Biswajit Sadhu, Henry Adams, Aurora Clark
Recent work (J. Chem. Phys. 154, 114114) has demonstrated that sublevelset persistent homology provides a compact representation of the complex features of an energy landscape in $3N$-dimensions. This includes information about all transition paths between local minima (connected by critical points of index > 1), and…
Charles Sing, Jian Qin
Complex coacervation is a phase separation phenomenon, driven by the electrostatic attraction between oppositely-charged macromolecular species. A recent surge of interest in coacervation between polyelectrolytes has been driven by both fundamental advances in experimental characterization of these systems, along with…
Wook Shin, Xinchun Ran, Xin Wang, Zhongyue Yang
Reaction dynamics trajectory simulations have been conducted to predict the product ratio of reactions with post-transition state bifurcation. However, it remains unknown how the entropy of reactive species along the reaction path mediates ambimodal selectivity. Here, by leveraging deep generative model, we developed…
Xinqiang Ding, John Drohan
A common approach for computing free energy differences among multiple states is to build a perturbation graph connecting the states and compute free energy differences on all edges of the graph. Such perturbation graphs are often designed to have cycles. Because free energy is a function of states, the free energy…
Anupam Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Amaro
Recent advances in computational power and algorithms have made molecular dynamics (MD) simulations reach greater timescales. However, for observing conformational transitions associated with biomolecular processes, MD simulations still have limitations. Several enhanced sampling techniques seek to address this…