Yroslav A. Kholodov

Innopolis University · Faculty of Computer Science and Engineering

Traffic congestion continues to pose a significant challenge in urban environments, necessitating innovative approaches to traffic management. This paper explores the application of Quantum Annealing (QA) for real-world traffic optimization, expanding on the pioneering work of Volkswagen and D-Wave. In 2017, a collaborative team demonstrated the po...

In this short paper, we describe natural logit population games dynamics that explain equilibrium models of origin-destination matrix estimation and (stochastic) traffic assignment models (Beckmann, Nesterov–de Palma). Composition of the proposed dynamics allows to explain two-stages traffic assignment models.

In this short paper we describe natural logit population games dynamics that explain equilibrium models of origin-destination matrix estimation and (stochastic) traffic assignment models (Beckmann, Nesterov--de Palma). Composition of the proposed dynamics allows to explain two-stages traffic assignment models.

Antibodies are key proteins produced by the immune system to target pathogen proteins termed antigens via specific binding to surface regions called epitopes. Given an antigen and the sequence of an antibody the knowledge of the epitope is critical for the discovery and development of antibody based therapeutics. In this work, we present a computat...

This paper presents a generalized second-order hydrodynamic traffic model. Its central piece is the expression for the relative velocity of the congestion (compression wave) propagation. We show that the well-known second-order models of Payne–Whitham, Aw–Rascal and Zhang are all special cases of the featured generalized model, and their properties...

In this paper, we compare various techniques to learn expressive product title embeddings starting from TF-IDF and ending with deep neural architectures. The problem is to recognize brands from noisy retail product names coming from different sources such as receipts and supply documents. In this work we consider product titles written in English a...

The template-based approach has been essential for achieving high-quality models in the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predicted Interactions). However, few such automated methods exist for protein-small molecule docking. In this paper, we present an algorithm for template-based docking of s...

In various applications arise problems modeled by nonlinear partial differential equations on graphs (networks, trees). In order to study such problems and various extreme situations arose in the problems of designing and optimizing networks developed the computational model based on solving the corresponding boundary problems for partial different...

Manifold representations of rotational/translational motion and conformational space of a ligand were previously shown to be effective for local energy optimization. In this paper we report the development of the Monte-Carlo energy minimization approach (MCM), which uses the same manifold representation. The approach was integrated into the docking...

A distinctive feature of hyperbolic equations is the finite propagation velocity of perturbations in the region of integration (wave processes) and the existence of characteristic manifolds: characteristic lines and surfaces (bounding the domains of dependence and influence of solutions). Another characteristic feature of equations and systems of h...

The localization of a vehicle is an important task in the field of intelligent transportation systems. It is well known that sensor fusion helps to create more robust and accurate systems for autonomous vehicles. Standard approaches, like extended Kalman Filter or Particle Filter, are inefficient in case of highly non-linear data or have high compu...

The short-term prediction of road traffic condition is one of the main tasks of transportation modelling. The main purpose of which are traffic control, reporting of accidents, avoiding traffic jams due to knowledge of traffic flow and subsequent transportation planning. A number of solutions exist - both model-driven and data driven had proven to...

In recent years, the localization of a vehicle has become an important task in the field of intelligent transportation systems (ITS). It is well known that sensor fusion helps to create more robust and accurate systems for autonomous vehicles. This paper presents a sensor fusion framework that combines trajectories built using global coordinates fr...

The objective of this study is the construction of the numerical mathematical model for the propagation of fine impurities in ventilation networks using gas dynamic equations by the numerical coupling of domains with different dimensions.

Significance Expressing the interaction energy as sum of correlation functions, fast Fourier transform (FFT) based methods speed the calculation, enabling the sampling of billions of putative protein–protein complex conformations. However, such acceleration is currently achieved only on a 3D subspace of the full 6D rotational/translational space, a...

Supporting Information Movie S1

Supporting Information

Supporting Information Movie S2

For quasilinear systems of hyperbolic equations, the nonclassical boundary value problem of controlling solutions with the help of boundary conditions is considered. Previously, this problem was extensively studied in the case of the simplest hyperbolic equations, namely, the scalar wave equation and certain linear systems. The corresponding proble...

Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the Cα -based protein model using the Truncated Expansion approximation (TEA) to the Rotne-Prager-Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (10(...

Method of Lagrange multipliers. (PDF)

Schematic of the setup used in nanoindentations in silico. The biological particle (virus shell) is placed on the substrate. The cantilever base (virtual sphere) is moving in the direction perpendicular to the surface of the particle with the constant velocity ν f (force-ramp), which creates a compressive force. The force is transmitted to the cant...

Graphical illustration of the coarse-graining procedure involved in construction of a SOP model of a polypeptide chain (see S1 Text). Panel (a) shows coarse-graining of the atomic structure of the protein subunit forming pentamers and capsomers of the CCMV shell (S1 Fig). Each amino acid residue is represented by a spherical bead of an appropriate...

Estimation of the thickness of TrV and AdV with encapsulated genome. (PDF)

Self Organized Polymer (SOP) model of a virus particle. (PDF)

SOP model parameterization for CCMV shell. (PDF)

Nanoindentation of the empty CCMV particle in silico (a) and in vitro (b). Shown in different colors for clarity are the FX curves obtained using the cantilever tip velocity ν f = 0.06 μm/s (experiment) and ν f = 1.0 μm/s (simulations). In the AFM-based experiments and in simulations of nanoindentation of CCMV, we used the cantilever tip with radiu...

Theoretical profile of the beam survival probability. Shown is the curve of s(X) obtained using Eq (16) with FNS model parameters for the empty CCMV particle tested experimentally (see Table 1 in the main text). The shaded area represents the width of the transition range ΔX ≈ 8.0 nm, which compares well with the experimental value of the same quan...

The structure of the Cowpea Chlorotic Mottle Virus (CCMV) (PDB code: 1CWP). The side view of the CCMV shell is shown on the right. The protein domains forming pentamers are in blue, while the same protein domains in hexamers are in red and orange. The hexamers and pentamers, composed of six and five copies of the same protein chain (circled in the...

AFM-based nanoindentation of the empty TrV particle (a), full TrV particle (encapsulating the single-stranded RNA genome; (b)) and full AdV particle (encapsulating the DNA genome, (c)). Shown in different colors for clarity are the representative force-deformation spectra. The FX curves for the empty TrV particle were obtained using the cantilever...

Dynamic force spectroscopy in silico: Forced indentation of CCMV capsid along the 2-fold symmetry axis. The movie shows the forced indentation experiment in silico on the CCMV shell, in which a compressive force is applied along the 2-fold symmetry axis (side view). The CCMV capsid is positioned on a solid mica surface (small gray colored beads). T...

In this paper we present a second-order hydrodynamic traffic model that generalizes the existing second-order models of Payne-Whithem, Zhang and Aw-Rascle. In the proposed model, we introduce the pressure equation describing the dependence of "traffic pressure" on traffic density. The pressure equation is constructed for each road segment from the...

In this paper, we propose a unified procedure for calibration of macroscopic second-order multilane traffic models. The focus is on calibrating the fundamental diagram using the combination stationary detector data and GPS traces. GPS traces are used in estimation of the deceleration wave speed. Thus calibrated model adequately represents the three...

In this paper, we propose the unified procedure for the development and calibration of mathematical model for multilane urban road traffic flow. We use macroscopic approach, describing traffic flow with the system of second-order nonlinear hyperbolic equations (for traffic density and velocity). We close the resulting model with the equation of veh...

The goal of this work is to generalize second order mathematical models for automotive flow using algorithm for building state equation - the dependency of pressure on traffic density - which is adequate with regard to real world data. The form of state equation, which closes the system of model equations, is obtained from experimental form of fund...

A novel efficient algorithm for searching for the optimum arrangement of two rigid bodies is proposed. Such a problem often arises in the analysis of the matching of three-dimensional shapes (e.g., in protein-protein docking). The proposed method is based on exhaustive enumeration of the possible arrangements in the spherical polar Fourier space an...

Изложены методы построения монотонных разностных схем высокого порядка аппроксимации для решения одномерных уравнений и систем гиперболического типа. Использование таких схем является актуальным при численном решении задач, содержащих в области интегрирования разрывы искомых функций и другие особенности. Навыки практического использования рассматри...

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physico-chemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using mu...

The purpose of this paper is to develop a macroscopic hydrodynamic model describing the vehicular traffic on a road junction and taking into account the distribution of traffic light phases and the existing road markings.

The transition from -helices to -strands under external mechanical force in fibrin molecule containing coiled-coils is studied and free energy landscape is resolved. The detailed theoretical modeling of each stage of coiled-coils fragment pulling process was performed. The plots of force (F) as a function of molecule expansion (X) for two symmetric...

The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling metho...

Algorithms of wireless sensor networks operation based on modified ZigBee/IEEE 802.15.4 protocol stack and problems of energy saving with simultaneous decrease of network latency are studied. Theoretical computations are given. Roles distribution and routers schedule assignment algorithms are described. Both results of experiments carried out with...

In this paper, data flows from different nodes in the packet network of data transmission are simulated as immiscible continuum flows. Conceptual and mathematical models are proposed. Computer simulation has been performed and compared with the ns-2 system of packet-level simulation. The developed model demonstrated fairly good accuracy, requiring...

The purpose of this paper is to generalize the macroscopic hydrodynamic vehicular traffic models by using the algorithm for constructing the adequate state equation - dependence the pressure from traffic density by taking into account the real experimental data (possibly using the parametric solutions for model equations). It is proved that this ki...

Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent require a reliable source of pseudorandom numbers generated at each step of calculation. We present the two main approaches for implementation of pseudorandom number generators on a GPU. In the first approach, inherent in CPU-based calculations, one PRNG...

Due to the very long timescales involved (ms-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programm...

The use of graphics processing units (GPUs) in simulation applications offers a significant speed gain as compared to computations on central processing units (CPUs). Many simulation methods require a large number of independent random variables generated at each step. We present two approaches for implementation of random number generators (RNGs)...

Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized pol...

The aim of research is to develop software system for solving gas dynamic problem in multiply connected integration domains of regular shape by high-performance computing system. Comparison of the various technologies of parallel computing has been done. The program complex is implemented using multithreaded parallel systems to organize both multi-...

Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent, widely used to access the microscopic transitions in biomolecules, require a reliable source of random numbers. Here we present the two main approaches for implementation of random number generators (RNGs) on a GPU, which enable one to generate random n...

Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programm...

Blood system functions are very diverse and important for most processes in human organism. One of its primary functions is matter transport among different parts of the organism including tissue supplying with oxygen, carbon dioxide excretion, drug propagation etc. Forecasting of these processes under normal conditions and in the presence of diffe...

Blood system functions are very diverse and important for most processes in human organism. One of its primary functions is matter transport among different parts of the organism including tissue supplying with oxygen, carbon dioxide excretion, drug propagation etc. Forecasting of these processes under normal conditions and in the presence of diffe...

Numerical model of the peripheral circulation and dynamical model of the large vessels and the heart are discussed in this paper. They combined together into the global model of blood circulation. Some results of numerical simulations concerning matter transport through the human organism and heart diseases are represented in the end.

Previously formulated monotonicity criteria for explicit two-level difference schemes designed for hyperbolic equations (S.K. Godunov’s, A. Harten’s (TVD schemes), characteristic criteria) are extended to multileveled, including implicit, stencils. The characteristic monotonicity criterion is used to develop a universal algorithm for constructing h...

For each graph edge with length Xk we consider 1D nonlinear hyperbolic system of equations n® t +F® xk ( n® ) = f® ,n® = { n1 , ¼,n1 },t \geqslant 0,0 \leqslant xk \leqslant Xk ,k = 1, ¼,K \overrightarrow \nu _t + \overrightarrow F _{x_k } \left( {\overrightarrow \nu } \right) = \overrightarrow f ,\overrightarrow \nu = \left\{ {\nu _1 , \ldots ,\...

The engineering structures composed from the rods (frames, trusses, etc.) are widely used in the various industrial applications. There are many publications presenting a theoretical modeling of the rod-based structural systems especially for the designs constructed from the thin-walled components. Usually, the single bar element of such system is...

In this paper the numerical investigation of parameters of the plasmoid expanding into rarefied ionosphere and the geomagnetic field are performed. The range of the initial energy change is ɛ∼1012–1015 [J]ɛ∼1012–1015 [J] and of the mass change is M=(0.3–1)⋅103 [kg]M=(0.3–1)⋅103 [kg]. These ranges conform to the well-known large-scale geophysical ex...

It was developed the 3D numerical MHD model meant for the simulation of the plasma cloud expansion into nonuniform partly ionized ionosphere with magnetic field. The plasma cloud has high energy density and was formed by the strong spherical explosion. The MHD equations were written down in the divergence form of one-speed and one-temperature appro...

The problems in the form of nonlinear partial derivative equations on graphs (nets, trees) arise in different applications. As the examples of such models we can name the circulatory and respiratory systems of the human body, the model of heavy traffic in the big cities, the model of flood water and pollution propagation in the large river systems,...

In the present paper a new method of construction of second and higher than second order of approximation monotone schemes for numerical solution of hyperbolic problems is proposed. It can be applied to a wide range of the Computational Fluid Dynamics problems. The numerical schemes obtained by this method have a number of important advantages. The...

In a large-scale geophysical experiment "Starfish" (weight of plasma 10 6 [g], energy 6*10 22 [erg]) the formation of an ascending plasma jet was observed where the most of the mass was distributed in the plane of a magnetic meridian. This kind of stream can be formed as the result of flutter mode growth on the front of the plasma stream. We create...