arXiv subjects

Takeshi Yamamoto

Publications and source records attributed to Takeshi Yamamoto.

5 recordsLinked to original sources

arXiv2026

Sequential replica exchange with solute tempering for atomistic modeling of supramolecular polymer structures

Predicting detailed atomistic structures of self-assembling systems remains a challenge for all-atom molecular dynamics simulations. Replica exchange with solute tempering (REST) has been used to study those systems by accelerating all monomers in a global and uniform manner. While such a global approach can in principle predict any morphology of the system, it has computational drawbacks such as inefficient replica traversal due to order-disorder transitions and the growing number of replicas with system size. To address these issues, here we propose an alternative, stepwise construction approach to modeling supramolecular polymers under the assumption of one-dimensional polymerization. Specifically, we generate polymer structures by adding new monomers one by one to the system and applying REST to the new monomers to find their optimal binding positions based on an energy-based scoring function. The monomer addition and enhanced sampling are repeated sequentially until a polymer of desired length is obtained. We test the above procedure using a model supramolecular polymer in explicit solvent, and show that it can generate a polymer structure with characteristic H-bonding patterns at reduced computational costs, while also improving the efficiency of replica traversal significantly. We thus expect that the sequential REST will be useful for modeling supramolecular polymers, particularly for cases where global REST simulations are too demanding computationally.

cond-mat.soft↗

arXiv2017

Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent, and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.

physics.chem-ph↗

arXiv2014

Observation of the "$K^-pp$"-like structure in the $d(π^+, K^+)$ reaction at 1.69 GeV/$c$

We have observed a "$K^-pp$"-like structure in the $d(π^+,K^+)$ reaction at 1.69 GeV/$c$. In this reaction $Λ(1405)$ hyperon resonance is expected to be produced as a doorway to form the $K^-pp$ through the $Λ^*p\rightarrow K^-pp$ process. However, most of the produced $Λ(1405)$'s would escape from deuteron without secondary reactions. Therefore, coincidence of high-momentum ($>$ 250~MeV/$c$) proton(s) in large emission angles ($39^\circ<θ_{lab.}<122^\circ$) was requested to enhance the signal-to-background ratio. A broad enhancement in the proton coincidence spectra are observed around the missing-mass of 2.27 GeV/$c^2$, which corresponds to the $K^-pp$ binding energy of 95 $^{+18}_{-17}$ (stat.) $^{+30}_{-21}$ (syst.) MeV and the width of 162 $^{+87}_{-45}$ (stat.) $^{+66}_{-78}$ (syst.) MeV.

nucl-ex↗

arXiv2008

Variational and perturbative formulations of QM/MM free energy with mean-field embedding and its analytical gradients

Conventional quantum chemical solvation theories are based on the mean-field embedding approximation. That is, the electronic wavefunction is calculated in the presence of the mean field of the environment. In this paper a direct quantum mechanical/molecular mechanical (QM/MM) analog of such a mean-field theory is formulated based on variational and perturbative frameworks. In the variational framework, an appropriate QM/MM free energy functional is defined and is minimized in terms of the trial wavefunction that best approximates the true QM wavefunction in a statistically averaged sense. Analytical free energy gradient is obtained, which takes the form of the gradient of effective QM energy calculated in the averaged MM potential. In the perturbative framework, the above variational procedure is shown to be equivalent with the first-order expansion of the QM energy (in the exact free energy expression) about the self-consistent reference field. This helps understand the relation between the variational procedure and the exact QM/MM free energy as well as existing QM/MM theories. Based on this, several ways are discussed for evaluating non-mean-field effects (i.e., statistical fluctuations of the QM wavefunction) that are neglected in the mean-field calculation. As an illustration, the method is applied to an SN2 Menshutkin reaction in water, NH3 + CH3CL -> NH3CH3^{+} + CL^{-}, for which free energy profiles are obtained at the HF, MP2, B3LYP, and BH&HLYP levels by integrating the free energy gradient. Non-mean-field effects are evaluated to be < 0.5 kcal/mol using a Gaussian fluctuation model for the environment, which suggests that those effects are rather small for the present reaction in water.

physics.chem-ph↗

arXiv2005

Path-integral virial estimator for reaction rate calculation based on the quantum instanton approximation

The quantum instanton approximation is a type of quantum transition state theory that calculates the chemical reaction rate using the reactive flux correlation function and its low order derivatives at time zero. Here we present several path-integral estimators for the latter quantities, which characterize the initial decay profile of the flux correlation function. As with the internal energy or heat capacity calculation, different estimators yield different variances (and therefore different convergence properties) in a Monte Carlo calculation. Here we obtain a virial-type estimator by using a coordinate scaling procedure rather than integration by parts, which allows more computational benefits. We also consider two different methods for treating the flux operator, i.e., local-path and global-path approaches, in which the latter achieves a smaller variance at the cost of using second-order potential derivatives. Numerical tests are performed for a one-dimensional Eckart barrier and a model proton transfer reaction in a polar solvent, which illustrates the reduced variance of the virial estimator over the corresponding thermodynamic estimator.

physics.chem-ph↗