Related papers: Implicit Ligand Theory: Rigorous Binding Free Ener…
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Response theory provides a pathway for understanding the sensitivity of a system and for predicting how its statistical properties change when a perturbation is applied. In the case of complex and multiscale systems, to achieve enhanced…
Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…
This works explores and illustrates recent results developed by the author in field of dynamical network analysis. The considered approach is blind, i.e., no a priori assumptions on the interconnected systems are available. Moreover, the…
We propose a structural equation model, which reduces to a multidimensional latent class item response theory model, for the analysis of binary item responses with non-ignorable missingness. The missingness mechanism is driven by two sets…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
In this paper, we further develop the approach, originating in [14 (arXiv:1311.6765),20 (arXiv:1604.02576)], to "computation-friendly" hypothesis testing and statistical estimation via Convex Programming. Specifically, we focus on…
We present a general embedding theory of electronic excitations of a relatively small, localized system in contact with an extended, chemically complex environment. We demonstrate how to include the screening response of the environment…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Linear receivers are often used to reduce the implementation complexity of multiple-antenna systems. In a traditional linear receiver architecture, the receive antennas are used to separate out the codewords sent by each transmit antenna,…
The process of deriving an interatomic potentials represents an attempt to integrate out the electronic degrees of freedom from the full quantum description of a condensed matter system. In practice it is the derivatives of the interatomic…
In this paper I apply newly-proposed information-theoretic principles to thermodynamic work extraction. I show that if it is possible to extract work deterministically from a physical system prepared in any one of a set of states, then…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Verifying entanglement with experimental measurements requires that we take the limitations of experimental techniques into account, while still proving that the data obtained could not have been generated from a classical source. In the…
Implicit feedback (e.g., clicks, dwell times, etc.) is an abundant source of data in human-interactive systems. While implicit feedback has many advantages (e.g., it is inexpensive to collect, user centric, and timely), its inherent biases…
The search for semiconductors with high thermoelectric figure of merit has been greatly aided by theoretical modeling of electron and phonon transport, both in bulk materials and in nanocomposites. Recent experiments have studied…
The design of online algorithms for matching markets and revenue management settings is usually bound by the assumption that the demand process is formed by a fixed-length sequence of queries with unknown types, each drawn independently.…