arXiv subjects

Donghyun Lee

Publications and source records attributed to Donghyun Lee.

62 records · Page 4Linked to original sources

arXiv2019

Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment

We present molecular mechanics {and spectroscopic} calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker, and Oregon Green 488, when these are attached at two different sites (104 and 123) on the TMV protein. The resulting geometric information shows that the extent of disorder and aggregation properties, and therefore the optical properties of the TMV-templated chromophore assembly, are highly dependent on the choice of chromophores and protein site to which they are bound. We used the results of the conformational search as geometric parameters together with an improved tight-binding Hamiltonian to simulate the linear absorption spectra and compare with experimental spectral measurements. The ideal dipole approximation to the Hamiltonian is not valid since the distance between chromophores can be very small. We found that using the geometries from the conformational search is necessary to reproduce the features of the experimental spectral peaks.

physics.chem-ph↗

arXiv2018

A Fast-Converged Acoustic Modeling for Korean Speech Recognition: A Preliminary Study on Time Delay Neural Network

In this paper, a time delay neural network (TDNN) based acoustic model is proposed to implement a fast-converged acoustic modeling for Korean speech recognition. The TDNN has an advantage in fast-convergence where the amount of training data is limited, due to subsampling which excludes duplicated weights. The TDNN showed an absolute improvement of 2.12% in terms of character error rate compared to feed forward neural network (FFNN) based modelling for Korean speech corpora. The proposed model converged 1.67 times faster than a FFNN-based model did.

cs.CL↗

arXiv2017

Uniform Regularity for free-boundary navier-stokes equations with surface tension

We study the zero-viscosity limit of free boundary Navier-Stokes equations with surface tension in $\mathbb{R}^3$ thus extending the work of Masmoudi and Rousset [1] to take surface tension into account. Due to the presence of boundary layers, we are unable to pass to the zero-viscosity limit in the usual Sobolev spaces. Indeed, as viscosity tends to zero, normal derivatives at the boundary should blow-up. To deal with this problem, we solve the free boundary problem in the so-called Sobolev co-normal spaces (after fixing the boundary via a coordinate transformation). We prove estimates which are uniform in the viscosity. And after inviscid limit process, we get the local existence of free-boundary Euler equation with surface tension. One of the main differences between this work and the work [1] is our use of time-derivative estimates and certain properties of the Dirichlet-Neumann operator. In a forthcoming work, we discuss how we can take the simultaneous limit of zero viscosity and surface tension [].

math.AP↗

arXiv2017

Initial value problem for the free boundary magnetohydrodynamics with zero magnetic boundary condition

We show local existence and uniqueness of plasma(fluid)-vaccum free boundary problem of magnetohydrodynamic flow in three-dimensional space with infinite depth setting when magnetic field is zero on the free boundary. We use Sobolev-Slobodetskii space which was used in usual free boundary problem in [3,5,6,7,8,9]. We also show that this solution can be extended as long as we want for sufficiently small initial data. Using the result of this paper we will get a unique solution of (kinematic inviscid) - (magnetic non diffusive) free boundary magnetohydrodynamics problem via (kinematic viscosity) - (magnetic diffusivity) limit in [10].

math.AP↗

arXiv2017

Uniform estimate of viscous free-boundary Magnetohydrodynamics with zero vacuum magnetic field

We consider viscous free-boundary magnetohydrodynamics(MHD) under vacuum in $\mathbb{R}^3$, especially when vacuum magnetic field is identically zero. It is a central problem in mathematics to perform vanishing viscosity limit to get a solution of hyperbolic inviscid system. However, boundary layer behavior happens near the free-boundary, so existence time $T^{\varepsilon} \rightarrow 0$ as kinematic viscosity $\varepsilon\rightarrow 0$ in standard sobolev space. Inspired by \cite{NMFR1}, we use sobolev conormal space to derive uniform regularity in viscosity $\varepsilon$. Finally, we get a solution of inviscid free-boundary magnetohydrodynamics when initial magnetic field is zero on the free-boundary and in vacuum.

math.AP↗

arXiv2017

Decay of the Boltzmann equation with the specular boundary condition in non-convex cylindrical domains

A basic question about the existence and stability of the Boltzmann equation in general non-convex domain with the specular reflection boundary condition has been widely open. In this paper, we consider cylindrical domains whose cross sections are general non-convex analytic planar domain. We establish the global-wellposedness and asymptotic stability of the Boltzmann equation with the specular reflection boundary condition in such domains. Our method consists of sharp classification of billiard trajectories which bounce infinitely many times or hit the boundary tangentially at some moment, and a delicate construction of an $\e$-tubular neighborhood of such trajectories. Analyticity of the boundary is crucially used. Away from such $\e$-tubular neighborhood, we control the number of bounces of trajectories and its' distance from singular sets in a uniform fashion. The worst case, sticky grazing set, can be excluded by cutting off small portion of the temporal integration. Finally we apply a method of \cite{KimLee} by the authors and achieve a pointwise estimate of the Boltzmann solutions.

math.AP↗

arXiv2016

The Boltzmann equation with specular boundary condition in convex domains

We establish the global-wellposedness and stability of the Boltzmann equation with the specular reflection boundary condition in general smooth convex domains when an initial datum is close to the Maxwellian with or without a small external potential. In particular, we have completely solved the long standing open problem after an announcement of [20] in 1977.

math.AP↗

arXiv2013

Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules in order to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers, and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models.

physics.chem-ph↗