1.5k citations · 1.7k across the 11 of their papers we have counts for
11 papers
A closed-form, analytical approximation for apparent surface charge and electric field of molecules
Dan Folescu, Alexey V. Onufriev
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. H…
Strongly bent double-stranded DNA: reconciling theory and experiment
Aleksander V. Drozdetski, Abhishek Mukhopadhyay, Alexey V. Onufriev
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the sa…
Multi-shell model of ion-induced nucleic acid condensation
Igor S. Tolokh, Aleksander Drozdetski, Lois Pollack +2
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by tri-valent cobalt(III) hexammine (CoHex) ions. The model is based on partitionin…
Understanding Nucleic Acid Structural Changes by Comparing Wide-Angle X-ray Scattering (WAXS) Experiments to Molecular Dynamics Simulations
Suzette A. Pabit, Andrea M. Katz, Igor S. Tolokh +4
Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known com…
The role of correlation and solvation in ion interactions with B-DNA
Maria L. Sushko, Dennis G. Thomas, Suzette A. Pabit +3
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous sm…
Accurate Evaluation of Charge Asymmetry in Aqueous Solvation
Abhishek Mukhopadhyay, Igor S. Tolokh, Alexey V. Onufriev
Charge hydration asymmetry (CHA)--a characteristic dependence of hydration free energy on the sign of the solute charge--quantifies the asymmetric response of water to electric fie…
Building Water Models, A Different Approach
Saeed Izadi, Ramu Anandakrishnan, Alexey V. Onufriev
Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despit…
Optimal Physical Multipoles
Charles Baker, Ramu Anandakrishnan, Alexey Onufriev
Point multipole expansions are widely used to gain physical insight into complex distributions of charges and to reduce the cost of computing interactions between such distribution…
Two-phase stretching of molecular chains
Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot +1
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here w…
Heat conductivity of DNA double helix
Alexander V. Savin, Mikhail A. Mazo, Irina P. Kikot +2
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on sim…
Memory Loss and Auger Processes in a Many Body Theory of Charge Transfer
A. V. Onufriev, J. B. Marston
Charge transfer between hyperthermal alkali atoms and metallic scattering surfaces is an experimental and theoretical arena for many-body interactions. To model new facets, we use…