arXiv subjects

Dilipkumar N. Asthagiri

Publications and source records attributed to Dilipkumar N. Asthagiri.

11 recordsLinked to original sources

arXiv2026

Large integration time-step in molecular dynamics simulation artificially enhances the strength of hydrophobic interaction

Molecular dynamics simulations are used to compute the potential of mean force (PMF) between two united-atom methane molecules at several temperatures and integration time-steps. At a fixed time-step, the contact minimum of the PMF deepens with increasing temperature, as expected for hydrophobicity driven association. Compared with a time-step of 0.5 fs, one that preserves equipartition, larger time-steps alter the PMF and make the contact minimum more favorable. Thus even relative free energy values are sensitive to time-steps that break equipartition. Using quasichemical theory, we partition the free energy of association into hydrophobic and hydrophilic contributions. The hydrophilic contribution opposes association and is insensitive to the time-step. Thus the artificial enhancement of association at larger time-steps comes entirely from the hydrophobic contribution. We explain this behavior through the temperature dependence of the internal pressure of the liquid. The same analysis also accounts for earlier observations of the liquid's p-V behavior under conditions that break equipartition.

cond-mat.soft↗

arXiv2026

Exploring the use of quantum computing for facilitating spatially and temporally resolved models of a biological cell

Whole-cell simulation, modeling all of a cell's functional systems over its life cycle, is an outstanding challenge in computational biology. Even the simplest living cell contains thousands of interacting proteins and metabolites (on the order of trillions of atoms) whose full functional dynamics spans roughly five orders of magnitude in space (nm to $μ$m) and nearly nineteen in time (fs to hours). Further, many of the governing physical and chemical properties remain incompletely characterized. Simulating such complex systems at fully atomistic resolution over a full cell cycle is computationally intractable on classical architectures, raising a central question: Can quantum computing offer a viable path to whole-cell simulations that integrate molecular- and systems-level complexity? This Perspective examines the potential of quantum computing across three hierarchical scales: atomistic-molecular modeling, metabolic and regulatory networks, and whole-cell spatial modeling. We present a complexity analysis comparing classical and quantum algorithms for representative biological problems, identifying regimes of substantial theoretical speedup under specified algorithmic assumptions. We highlight algorithmic developments designed to leverage both near-term exploratory and fault-tolerant quantum architectures, and discuss practical bottlenecks: data encoding overhead, system conditioning, measurement constraints, and hybrid quantum-HPC integration. Together, these results outline a roadmap for quantum-accelerated whole-cell modeling and the biological insights such multiscale frameworks may eventually enable.

quant-ph↗

arXiv2026

Rotational Memory Function of SPC/E water

Memory effects are essential for dynamics of condensed materials and are responsible for non-exponential relaxation of correlation functions of dynamic variables through the memory function. Memory functions of dipole rotations for polar liquids have never been calculated. We present here calculations of memory functions for single-dipole rotations and for the overall dipole moment of the sample for SPC/E water. The memory functions for single-particle and collective dipole dynamics turn out to be nearly identical. This result validates theories of dielectric spectroscopy in terms of single-particle time correlation functions and the connection between the collective and single-particle relaxation times through the Kirkwood factor. The dielectric function in this formalism contains no new dynamic information that does not exist in the single-dipole correlation function. A short memory time, $\lesssim 1$ fs, justifies the use of rotational diffusion model to describe dynamics of a single molecular dipole moment in bulk water.

cond-mat.stat-mech↗

arXiv2025

Equipartition and the temperature of maximum density of TIP4/2005 water

We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps $δ=$ 0.25, 0.50, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or 0.50 fs are in excellent agreement with each other but differ from those obtained using time-steps that have been shown earlier to lead to a breakdown of equipartition. The temperature of maximum density (TMD) is 277.15 K with $δt = 0.25\;\mathrm{or}\; 0.50$ fs, but is shifted to progressively lower values for longer time-steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water-water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid-vapor phase envelope. A key takeaway from this study is that using sufficiently short time-steps ($\leq 0.5$ fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable data to parametrize biomolecular simulation models, as correct-ensemble sampling is fundamental to ensure reproducibility across codes and simulation alogrithms.

cond-mat.soft↗

arXiv2025

Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein

Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step $δt \leq 0.5$ fs to ensure equipartition between translational and rotational modes. Here we extend that study in the $NVT$ ensemble to $NpT$ conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examine integration time-steps ranging from $0.5$ fs to $4.0$ fs for various thermostat plus barostat combinations. We find that a small $δt$ is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to $δt$. Using the mean volume estimated from the $NpT$ simulation, we examine the electrostatic and van der Waals contribution to the hydration free energy of the protein in the $NVT$ ensemble. These contributions are also sensitive to $δt$. In going from $δt = 2$ fs to $δt = 0.5$ fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein.

cond-mat.soft↗

arXiv2024

Quantifying the Errors Introduced by Continuum Scattering Models on the Inferred Structural Properties of Proteins

Atomistic force fields that are tuned to describe folded proteins predict overly compact structures for intrinsically disordered proteins (IDPs). To correct this, improvements in force fields to better model IDPs are usually paired with scattering models for validation against experiments. For scattering calculations, protein configurations from all-atom simulations are used within the continuum-solvent model CRYSOL for comparison with experiments. To check this approach, we develop an equation to evaluate the radius of gyration (Rg) for any defined inner-hydration shell thickness given all-atom simulation data. Rg based on an explicit description of hydration waters compares well with the reference value of Rg obtained using Guinier analysis of the all-atom scattering model. However, these internally consistent estimates disagree with Rg from CRYSOL for the same definition of the inner-shell. CRYSOL can over-predict Rg by up to 2.5 Angstroms. We rationalize the reason for this behavior and highlight the consequences for force field design.

physics.chem-ph↗

arXiv2024

Theory and modeling of molecular modes in the NMR relaxation of fluids

Traditional theories of the NMR autocorrelation function for intramolecular dipole pairs assume single-exponential decay, yet the calculated autocorrelation of realistic systems display a rich, multi-exponential behavior resulting in anomalous NMR relaxation dispersion (i.e., frequency dependence). We develop an approach to model and interpret the multi-exponential autocorrelation using simple, physical models within a rigorous statistical mechanical development that encompasses both rotational and translational diffusion in the same framework. We recast the problem of evaluating the autocorrelation in terms of averaging over a diffusion propagator whose evolution is described by a Fokker-Planck equation. The time-independent part admits an eigenfunction expansion, allowing us to write the propagator as a sum over modes. Each mode has a spatial part that depends on the specified eigenfunction, and a temporal part that depends on the corresponding eigenvalue (i.e., correlation time) with a simple, exponential decay. The spatial part is a probability distribution of the dipole-pair, analogous to the stationary states of a quantum harmonic oscillator. Drawing inspiration from the idea of inherent structures in liquids, we interpret each of the spatial contributions as a specific molecular mode. These modes can be used to model and predict NMR dipole-dipole relaxation dispersion of fluids by incorporating phenomena on the molecular level. We validate our statistical mechanical description of the distribution in molecular modes with molecular dynamics simulations interpreted without any relaxation models or adjustable parameters: the most important poles in the Pad{é}-Laplace transform of the simulated autocorrelation agree with the eigenvalues predicted by the theory.

physics.chem-ph↗

arXiv2023

Equilibration between Translational and Rotational Modes in Molecular Dynamics Simulations of Rigid Water Requires a Smaller Integration Time-Step Than Often Used

In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $δt$ for integrating the equations of motion. Thus $δt = 2$ fs is often used in simulating rigid models of water. We simulate the SPC/E model of water using $δt$ from 0.5 fs to 3.0 fs. We find that for all but $δ= 0.5$ fs, equipartition between translational and rotational modes is violated: the rotational modes are at a lower temperature than the translation modes. The autocorrelation of the velocities corresponding to the respective modes shows that the rotational relaxation occurs at a time-scale comparable to vibrational periods, invalidating the original assumption for freezing vibrations. $δt$ also influences thermodynamic properties: the mean system potential energies are not converged until $δt = 0.5$ fs, and the excess entropy of hydration of a soft, repulsive cavity is also sensitive to $δt$.

cond-mat.soft↗

arXiv2022

Hydrated anions: From clusters to bulk solution with quasi-chemical theory

The interactions of hydrated ions with solution and interface partners are strong on a chemical energy scale. Here, we test the foremost \textit{ab initio theory} for evaluation of hydration free energies of ions, namely, \textit{quasi-chemical theory} (QCT). We focus on halide anions, but also the hydroxide anion, since they have been outstanding challenges for all theories. QCT is built by identification of inner-shell clusters, separate treatment of those clusters, then integration of those results into the broader-scale solution environment. We exploit a close comparison with mass-spectrometric measurements of ion-hydration equilibria. That theory-experiment comparison is excellent with moderate computational effort here. This agreement reinforces both theory and experiment, and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. QCT provides a favorable setting for exploitation of the polarizable continuum model (PCM) when the inner-shell material shields the ion from the outer solution environment. For the asymmetrically hydrated, and less effectively shielded, heavier halide ions, we investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement and our final results are in close agreement with a standard tabulation of hydration free energies. Comparison of anion hydration cluster structures with bulk solutions from AIMD simulations emphasize slight differences: the asymmetries of bulk solution inner-shell structures are moderated, but still present; and inner shells fill to slightly higher average coordination numbers in bulk solution than in clusters.

physics.chem-ph↗

arXiv2022

Hydration free energies of polypeptides from popular implicit solvent models versus all-atom simulation results based on molecular quasichemical theory

The hydration free energy of a macromolecule is the central property of interest for understanding its distribution over conformations and its state of aggregation. Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT), an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecule solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions, and thus provides a convenient framework to investigate the assumptions in implicit-solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit-solvent models for poly-glycine and poly-alanine solutes covering a range of chain lengths and conformations. Among the three models, GB/SA does best in capturing the broad trends in hydration free energy. We trace the deficiencies of the group-additive EEF1 and ABSINTH models to their under-appreciation of the cooperativity of hydration between solute groups; seen in this light, the better performance of GB/SA can be attributed to its treatment of the collective properties of hydration, albeit within a continuum dielectric framework. We highlight the importance of validating the individual physical components that enter implicit solvent models for protein solution thermodynamics.

cond-mat.soft↗

arXiv2021

Thermodynamics of Hydration from the Perspective of the Molecular Quasi-Chemical Theory of Solutions

The quasi-chemical organization of the potential distribution theorem -- molecular quasi-chemical theory (QCT) -- enables practical calculations and also provides a conceptual framework for molecular hydration phenomena. QCT can be viewed from multiple perspectives: (a) As a way to regularize an ill-conditioned statistical thermodynamic problem; (b) As an introduction of and emphasis on the neighborship characteristics of a solute of interest; (c) Or as a way to include accurate electronic structure descriptions of near-neighbor interactions in defensible statistical thermodynamics by clearly defining neighborship clusters. The theory has been applied to solutes of a wide range of chemical complexity, ranging from ions that interact with water with both long-ranged and chemically intricate short-ranged interactions, to solutes that interact with water solely through traditional van~der~Waals interations, and including water itself. The solutes range in variety from monoatomic ions to chemically heterogeneous macromolecules. A notable feature of QCT is that in applying the theory to this range of solutes, the theory itself provides guidance on the necessary approximations and simplifications that can facilitate the calculations. In this Perspective, we develop these ideas and document them with examples that reveal the insights that can be extracted using the QCT formulation.

physics.chem-ph↗