相关论文: Reaction Coordinates for Conformational Transition…
LDA+DMFT is a novel computational technique for ab initio investigations of real materials with strongly correlated electrons, such as transition metals and their oxides. It combines the strength of conventional band structure theory in the…
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 chapter, we present CORrelation ALignment (CORAL), a simple yet effective method for unsupervised domain adaptation. CORAL minimizes domain shift by aligning the second-order statistics of source and target distributions, without…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Strong field photoemission and electron recollision provide a viable route to extract electronic and nuclear dynamics from molecular targets with attosecond temporal resolution. However, since an {\em ab-initio} treatment of even the…
Computational prediction of enzymatic reactions represents a crucial challenge in sustainable chemical synthesis across various scientific domains, ranging from drug discovery to materials science and green chemistry. These syntheses rely…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component…
A new class of matching condition between the atomistic and continuum regions is presented for the multi-scale modeling of crystals. They ensure the accurate passage of large scale information between the atomistic and continuum regions and…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
This paper investigates how Transformer language models (LMs) fine-tuned for acceptability classification capture linguistic features. Our approach uses the best practices of topological data analysis (TDA) in NLP: we construct directed…
The manipulation of the motion of neutral molecules with electric or magnetic fields has seen tremendous progress over the last decade. Recently, these techniques have been extended to the manipulation of large and complex molecules. In…
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involved in these processes, and (ii) estimation of the rates or…
An observed broad resonance peak in dissociative electron attachment (DEA) cross sections to a molecule might be due to either closely lying or overlapping resonances involved in the process. We developed a state-of-the-art experimental…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Effective dynamics using conditional expectation was proposed in [F. Legoll and T. Leli\`evre, Nonlinearity, 2010] to approximate the essential dynamics of high-dimensional diffusion processes along a given reaction coordinate. The…
Beyond the dielectric continuum description initiated by Marcus theory, the nowadays standard theoretical approach to study electron transfer (ET) reactions in solution or at interfaces is to use classical force field or ab initio Molecular…
The nonlinear optical response of a system of molecules often contains contributions whereby the products of lower-order processes in two separate molecules give signals that appear on top of a genuine direct higher-order process with a…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Realistic nuclear level densities (NLDs) obtained within the spectral distribution method (SDM) are employed to study nuclear processes of astrophysical interest. The merit of SDM lies in the fact that the NLDs corresponding to many body…