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+34 946 567 842
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+34 946 567 842
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eakhmatskaya@bcamath.org
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Profile at Ikerbasque Berkeley Lab QMMMy major research interest is in the development of numerical methods for modelling and simulation of complex systems. The main features of my research career have been: Work on the interface of Mathematics, Biology, Chemistry, Physics, Computational Statistics and Computer Science
Broad diapason of research activities from developing theoretical methods and implementing them on high performance, computers to application of software codes for study of important phenomena and processes.
Collaboration with multiinternational academic and industrial partners (Oxford University (UK), Imperial College London (UK), St Andrews University (UK), Berkeley Labs (USA), Accelrys Inc. (USA), NAG (UK), POLYMAT (Spain), energiGUNE (Spain), bioGUNE (Spain) among others).
Work experience:
 Academic: Cornell University, USA; University of Manchester, Imperial College, UK.
 Industrial: Fujitsu Centre for Information Technology, UK. Fujitsu Laboratories of Europe, UK.

A macroscopic clock model to solve the paradox of Schrödinger’s cat
(20241201)We propose detecting the moment an atom emits a photon by means of a nearly classical macroscopic clock and discuss its viability. It is shown that what happens in such a measurement depends on the relation between the ...

Adaptive multistage integration schemes for Hamiltonian Monte Carlo
(20240126)Hamiltonian Monte Carlo (HMC) is a powerful tool for Bayesian statistical inference due to its potential to rapidly explore high dimensional state space, avoiding the random walk behavior typical of many Markov Chain Monte ...

A datamining approach to understanding the impact of multidoping on the ionic transport mechanism of solid electrolytes materials: the case of dualdoped Ga<inf>0.15</inf>/Sc<inf>y</inf> Li<inf>7</inf>La<inf>3</inf>Zr<inf>2</inf>O<inf>12</inf>
(20240119)This study presents novel computational methods applied to the technologically significant solid electrolyte materials, Li6.55+yGa0.15La3Zr2−yScyO12 (Ga0.15/ScyLLZO), in order to investigate the effect of the distribution ...

The crystal chemistry and reactivity of ternary Na2Fe3Cl8 from the NaClFeCl2 system and its potential application as coating layer for cathode in sodium ion batteries
(20231215)This report explores theoretical and experimental methods to characterize the ternary phases arising from the NaCl + FeCl2 system at both low (150 °C) and high temperatures (550 °C), through milling and evaporation processing ...

BayFlux: A Bayesian Method to Quantify Metabolic Fluxes and their Uncertainty at the Genome Scale.
(20231110)Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13C Metabolic Flux Analysis (13C MFA) is considered to ...

A Novel Mathematical Approach for Analysis of Integrated Cell–Patient Data Uncovers a 6Gene Signature Linked to Endocrine Therapy Resistance
(20231109)A significant number of breast cancers develop resistance to hormone therapy. This progression, while posing a major clinical challenge, is difficult to predict. Despite important contributions made by cell models and ...

Anion Trapping and Ionic Conductivity Enhancement in PEOBased Composite PolymerLi<inf>7</inf>La<inf>3</inf>Zr<inf>2</inf>O<inf>12</inf> Electrolytes: The Role of the Garnet Li Molar Content
(20230613)The successful development of allsolidstate batteries will provide solutions for many problems facing current Liion batteries, such as high flammability, limited energy density, poor cyclability and low cation transference ...

Reducing Model Complexity by Means of the Optimal Scaling: Population Balance Model for Latex Particles Morphology Formation.
(20230415)Rational computeraided design of multiphase polymer materials is vital for rapid progress in many important applications, such as: diagnostic tests, drug delivery, coatings , additives for constructing materials, cosmetics, ...

A HighQuality GenomeScale Model for Rhodococcus opacus Metabolism
(2023)Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genomescale model (GSM) of R. opacus PD630 ...

On the interfacial lithium dynamics in Li7La3Zr2O12:poly(ethylene oxide) (LiTFSI) composite polymerceramic solid electrolytes under strong polymer phase confinement
(20220527)A better molecularlevel understanding of Li+ diffusion through ceramic/polymer interfaces is key to designing highperformance composite solidstate electrolytes for allsolidstate batteries. By considering as a case ...

Numerical Regge pole analysis of resonance structures in statetostate reactive differential cross sections
(20220419)This is the third (and the last) code in a collection of three programs [Sokolovski et al. (2011), Akhmatskaya et al. (2014)] dedicated to the analysis of numerical data, obtained in an accurate simulation of an atomdiatom ...

Wigner's friends, tunnelling times and Feynman's "only mystery of quantum mechanics"
(20220113)Recent developments in elementary quantum mechanics have seen a number of extraordinary claims regarding quantum behaviour, and even questioning internal consistency of the theory. These are, we argue, different disguises ...

Unveiling Interfacial LiIon Dynamics in Li7La3Zr2O12/PEO(LiTFSI) Composite PolymerCeramic Solid Electrolytes for AllSolidState Lithium Batteries
(20210623)Unlocking the full potential of solidstate electrolytes (SSEs) is key to enabling safer and moreenergy dense technologies than today’s Liion batteries. In particular, composite materials comprising a conductive, flexible ...

Tunnelling times, Larmor clock, and the elephant in the room
(20210511)A controversy surrounding the “tunnelling time problem” stems from the seeming inability of quantum mechanics to provide, in the usual way, a definition of the duration a particle is supposed to spend in a given region of ...

Multiscale Modelling and Simulation of Advanced Battery Materials
(2021)Development of efficient strategies for the rational design of materials involved in the production and storage of renewable energy is essential for accelerating the transition to a lowcarbon economy. To contribute to ...

An optimal scaling to computationally tractable dimensionless models: Study of latex particles morphology formation
(202002)In modelling of chemical, physical or biological systems it may occur that the coefficients, multiplying various terms in the equation of interest, differ greatly in magnitude, if a particular system of units is used. Such ...

Exploring Liion conductivity in cubic, tetragonal and mixedphase Alsubstituted Li7La3Zr2O12 using atomistic simulations and effective medium theory
(20190815)Garnet Li7La3Zr2O12 (LLZO) is a promising solid electrolyte candidate for solidstate Liion batteries, but at room temperature it crystallizes in a poorly Liion conductive tetragonal phase. To this end, partial substitution ...

Modified Hamiltonian Monte Carlo for Bayesian Inference
(20190722)The Hamiltonian Monte Carlo (HMC) method has been recognized as a powerful sampling tool in computational statistics. We show that performance of HMC can be significantly improved by incorporating importance sampling and ...

No Time at the End of the Tunnel
(20180821)Modern attosecond experiments seek to provide an insight into a long standing question: “how much time does a tunnelling particle spend in the barrier?” Traditionally, quantum theory relates this duration to the delay ...

Multistage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods
(20180717)Modified Hamiltonian Monte Carlo (MHMC) methods combine the ideas behind two popular sampling approaches: Hamiltonian Monte Carlo (HMC) and importance sampling. As in the HMC case, the bulk of the computational cost of ...

Revealing the Mechanism of Sodium Diffusion in NaxFePO4 Using an Improved Force Field
(20180402)Olivine NaFePO4 is a promising cathode material for Naion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalationdeintercalation processes, yet little is known about Na+ diffusion ...

Atomistic Insight into Ion Transport and Conductivity in Ga/AlSubstituted Li$_7$La$_3$Zr$_2$O$_{12}$ Solid Electrolytes
(20180109)Garnetstructured Li$_{7}$La$_{3}$Zr$_{2}$O$_{12}$ is a promising solid electrolyte for nextgeneration solidstate Li batteries. However, sufficiently fast Liion mobility required for battery applications only emerges ...

An even simpler understanding of quantum weak values
(201801)We explain the properties and clarify the meaning of quantum weak values using only the basic notions of elementary quantum mechanics.

Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation
(20171024)The modified Hamiltonian Monte Carlo (MHMC) methods, i.e., importance sampling methods that use modified Hamiltonians within a Hybrid Monte Carlo (HMC) framework, often outperform in sampling efficiency standard techniques ...

Reexamination of continuous fuzzy measurement on twolevel systems
(20170410)Imposing restrictions on the Feynman paths of the monitored system has in the past been proposed as a universal modelfree approach to continuous quantum measurements. Here we revisit this proposition and demonstrate that ...

Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO$_4$
(20170307)The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum, atomistic and mesoscales. The methods accessing these scales not only have to be effective but ...

Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials
(20170101)Computationaldriven materials discovery requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFTbased methods have limitations. One ...

Adaptive multistage integrators for optimal energy conservation in molecular simulations
(20161001)We introduce a new Adaptive Integration Approach (AIA) to be used in a wide range of molecular simulations. Given a simulation problem and a step size, the method automatically chooses the optimal scheme out of an available ...

Numerical simulation of extreme wave runup during storm events in Tramandaí Beach, Rio Grande do Sul, Brazil
(20151231)We present a high resolution analysis of the interaction of irregular waves with natural and urban structures leading to extreme wave runup. Horizontal runup data, instantaneous flooding maps, and wave propagation beyond ...

Relative frequencies of constrained events in stochastic processes: An analytical approach
(20151231)The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They relies on knowledge of interevent probability density ...

Complex angular momentum theory of statetostate integral cross sections: Resonance effects in the $F + HD \to HF(v' = 3) + D$ reaction
(20151231)Statetostate reactive integral cross sections (ICSs) are often affected by quantum mechanical resonances, especially near a reactive threshold. An ICS is usually obtained by summing partial waves at a given value of ...

NonMarkovian models of the growth of a polymer chain
(20151231)Using simple exactly solvable models, we show that eventdependent time delays may lead to significant nonPoisson effects in the statistics of polymer chain growth. The results are confirmed by stochastic simulation of ...

Multipletimestepping generalized hybrid Monte Carlo methods
(20141231)Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [24], molecular dynamics and hybrid Monte Carlo, can be further improved ...

Constant pressure hybrid Monte Carlo simulations in GROMACS
(20141231)Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPTGSHMC, combines ...

Impact of competitive processes on controlled radical polymerization
(20141231)The kinetics of radical polymerization have been systematically studied for nearly a century and in general are well understood. However, in light of recent developments in controlled radical polymerization many kinetic ...

Computer software for understanding resonances and resonancerelated phenomena in chemical reactions
(20141231)In numerical modelling of chemical reactions one calculates the scattering matrix for the required values of energy and angular momentum. Having done so, one still faces the nontrivial task of extracting detailed information ...

Numerical Regge pole analysis of resonance structures in elastic, inelastic and reactive statetostate integral cross sections
(20141231)We present a detailed description of a FORTRAN code for evaluation of the resonance contribution a Regge trajectory makes to the integral statetostate cross section (ICS) within a specified range of energies. The ...

'Superluminal paradox' in wave packet propagation and its quantum mechanical resolution
(20131231)We analyse in detail the reshaping mechanism leading to apparently 'superluminal' advancement of a wave packet traversing a classically forbidden region. In the coordinate representation, a barrier is shown to act as an ...

Interference mechanism of seemingly superluminal tunneling
(20131231)Apparently "superluminal" transmission, e.g., in quantum tunneling and its variants, occurs via a subtle interference mechanism which allows reconstruction of the entire spatial shape of a wave packet from its front tail. ...

Dynamic modeling of the morphology of multiphase waterborne polymer particles
(20131231)Multiphase waterborne polymer particles provide advantages in more demanding applications, and their performance depends on particle morphology. Currently, no dynamic model for the prediction of the development of the ...

Combining stochastic and deterministic approaches within high efficiency molecular simulations
(20131231)Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). ...

Particle Morphology
(20131231)This chapter discusses the morphology of latex particles obtained mainly by (mini)emulsion polymerisation. It describes some applications of these particles, and discusses the factors that influence the particle morphology. ...

Molecular dynamics simulations of iron and aluminumloaded serum transferrin: Protonation of tyr188 is necessary to prompt metal release
(20121231)Serum transferrin (sTf) carries iron in blood serum and delivers it into cells by receptormediated endocytosis. The protein can also bind other metals, including aluminum. The crystal structures of the metalfree and ...

Dynamic modeling of the morphology of latex particles with in situ formation of graft copolymer
(20121231)Modification of the polymerpolymer interfacial tension is a way to tailormake particle morphology of waterborne polymerpolymer hybrids. This allows achieving a broader spectrum of application properties and maximizing ...

Multiscale simulations of the antimicrobial peptide maculatin 1.1: Water permeation through disordered aggregates
(20121231)The antimicrobial peptide maculatin 1.1 (M1.1) is an amphipathic αhelix that permeabilizes lipid bilayers. In coarsegrained molecular dynamics (CG MD) simulations, M1.1 has previously been shown to form membranespanning ...

Causality, 'superluminality', and reshaping in undersized waveguides
(20121231)We analyse the reshaping mechanism leading to apparently 'superluminal' advancement of a pulse traversing an undersized section of a waveguide. For frequencies below the first inelastic threshold (cut off one), there are ...

Classification of resonance Regge trajectories and a modified Mulholland formula
(20111231)We employ a simple potential model to analyze the effects which a Regge trajectory, correlating with a bound or a metastable state at zero angular momentum, has on an integral cross section. A straightforward modification ...

Extracting Smatrix poles for resonances from numerical scattering data: TypeII Padé reconstruction
(20111231)We present a FORTRAN 77 code for evaluation of resonance pole positions and residues of a numerical scattering matrix element in the complex energy (CE) as well as in the complex angular momentum (CAM) planes. Analytical ...

Hartman effect and weak measurements that are not really weak
(20111231)We show that in wave packet tunneling, localization of the transmitted particle amounts to a quantum measurement of the delay it experiences in the barrier. With no external degree of freedom involved, the envelope of the ...

MesoGSHMC: A stochastic algorithm for mesoscale constant temperature simulations
(20111231)We consider the problem of timestepping/sampling for molecular and mesoscale particle dynamics. The aim of the work is to derive numerical timestepping methods that generate samples exactly from the desired target ...
Extracting Smatrix poles for resonances from numerical scattering data: typeII Padé reconstruction(PADE II)
The code is designed for evaluation of resonance pole positions and residues of a numerical scattering matrix element in the complex energy (CE) as well as in the complex angular momentum (CAM) planes. Analytical continuation of the Smatrix element is performed by constructing a typeII Pade approximant from given physical values. The algorithm involves iterative ‘preconditioning’ of the numerical data by extracting its rapidly oscillating potential phase component. The code has the capability of adding nonanalytical noise to the numerical data in order to select ‘true’ physical poles, investigate their stability and evaluate the accuracy of the reconstruction. It has an option of employing multipleprecision (MPFUN) package developed by D.H. Bailey wherever double precision calculations fail due to a large number of input partial waves (energies) involved.
Authors: Elena Akhmatskaya
License: the CPC nonprofit use license agreement  Mendeley Data
Numerical Regge pole analysis of resonance structures in statetostate reactive differential cross sections (DCS_Regge)
This is the third (and the last) code in a collection of three programs [Sokolovski et al. (2011), Akhmatskaya et al. (2014)] dedicated to the analysis of numerical data, obtained in an accurate simulation of an atomdiatom chemical reaction. Our purpose is to provide a detailed complex angular momentum (CAM) analysis of the resonance effects in reactive angular scattering. The code evaluates the contributions of a Regge trajectory (or trajectories) to a differential cross section in a specified range of energies. The contribution is computed with the help of the methods described in [Dobbyn et al. (1999), Sokolovski and Msezane (2004), Sokolovski et al. (2007)]. Regge pole positions and residues are obtained by analytically continuing Smatrix element, calculated numerically for the physical integer values of the total angular momentum, into the complex angular momentum plane using the PADE_II program [Sokolovski et al. (2011)]. The code represents a reactive scattering amplitude as a sum of the components corresponding to a rapid “direct” exchange of the atom, and the various scenarios in which the reactants form longlived intermediate complexes, able to complete several rotations before breaking up into products.
Authors: Elena Akhmatskaya
License: the CPC nonprofit use license agreement  Mendeley Data
Numerical Regge pole analysis of resonance structures in elastic, inelastic and reactive statetostate integral cross sections (ICS_Regge)
ICS_Regge is a suite of FORTRAN codes for evaluation of the resonance contribution a Regge trajectory makes to the integral statetostate cross section (ICS) within a specified range of energies. The contribution is evaluated with the help of the Mulholland formula (Macek et al., 2004) and its variants (Sokolovski et al., 2007; Sokolovski and Akhmatskaya, 2011). Regge pole positions and residues are obtained by analytically continuing Smatrix element, evaluated numerically for the physical values of the total angular momentum, into the complex angular momentum plane using the PADE_II program (Sokolovski et al., 2011). The code decomposes an elastic, inelastic, or reactive ICS into a structured, resonance, and a smooth, ‘direct’, components, and attributes observed resonance structure to resonance Regge trajectories.
Authors: Elena Akhmatskaya
License: the CPC nonprofit use license agreement  Mendeley Data
Date  Title  Number  Author/s  Status 

20131119  A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System  8589127  E. V. Akhmatskaya, S. Reich  
20130813  A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System Using Shadow Hamiltonians  8510084  E. V. Akhmatskaya, S. Reich  
20130528  Method, Apparatus and Computer Program for Simulating Behaviour of Thermodynamic Systems  US 8452576  S. Reich, E. V. Akhmatskaya, R. H. Nobes  
20110305  Method, Apparatus and Computer Program for Molecular Simulation  US007908129  E. V. Akhmatskaya, R. H. Nobes, S. Reich  
20110112  A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System  EP2273395 (A1)  E. V. Akhmatskaya, S. Reich  Published 
20110112  A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System Using Shadow Hamiltonians  EP2273396 (A1)  E. V. Akhmatskaya, S. Reich  Published 
20100203  Method, Apparatus and Computer Program for Simulating Behaviour of Thermodynamic Systems  GB 2462261 A  S. Reich, E. V. Akhmatskaya, R. H. Nobes  Published 
20090211  Method, Apparatus and Computer Program for Molecular Simulation  GB 2451701 A  E. V. Akhmatskaya, S. Reich, R. H. Nobes  Published 

 An Introduction to Monte Carlo methods: Extensions, Variations and Applications of Monte Carlo Method  BCAM & UPV/EHU Courses 20122013 (BCAM)
 Workshop on Dynamical Systems and Applications, Bilbao, Basque Country  Member of Scientific Committee  1011December, 2013
 9th American Institute of Mathematical Sciences International Conference on Dynamical Systems and Differential Equations (AIMS 2012), Orlando, USA  Special Session Organizer  15 July, 2012
 Minisymposium on Nonlinear dynamics applied to biological modelling, Bilbao, Basque Country  Member of Organizing Committee  09 February, 2012
 The Second HPCGA Workshop, Bilbao, Basque Country  Member of Organizing Committee  1115 March, 2013
 Quantum Days in Bilbao IV: Mathematical Methods in Atomic and Molecular Physics, Bilbao, Spain  Organizer  1516 July, 2014
 10th American Institute of Mathematical Sciences Conference on Dynamical Systems, Differential Equations and Applications (AIMS 2014), Madrid, Spain  Special Session Organizer  0711 July, 2014
 The International Conference on Scientific Computation and Differential Equations, SciCADE 2015, Enhanced Sampling Methods, Minisymposium, Potsdam, Germany  Special Session Organizer  1418 September, 2015
 Quantum Days in Bilbao V: Mathematical Methods in Atomic and Molecular Physics  Satellite of QRS XIII, Bilbao, Spain  Organizer  1314 July, 2015
 BCAM  IMUVA Summer School on Uncertainty Quantification for Applied Problems, Bilbao, Basque Country, Spain  Organizer  47 July, 2016
 131st European Study Group with Industry (ESGI), Bilbao, Basque Country, Spain  Member of Scientific Committee  1519 May, 2017
 Minisymposium "Advances in Modelling Multiscale Systems and their Applications", the VIII International Conference on Coupled Problems in Science and Engineering, Coupled 2019, Sitges, Spain  Organizer  3 June, 2019  5 August, 2019
 International Summer School on Fractional and Other Nonlocal Models, Bilbao, Basque Country, Spain  Organizer  2831 May, 2018
 150th European Study Group with Industry (ESGI), Bilbao, Basque Country, Spain  Member of Scientific Committee  2125 October, 2019