## About

64

Publications

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1,979

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Introduction

Additional affiliations

February 2021 - February 2021

July 2018 - present

May 2014 - July 2018

Education

January 2007 - October 2010

October 2001 - November 2006

## Publications

Publications (64)

Many scientific applications are inherently multiscale in nature. Such complex physical phenomena often require simultaneous execution and coordination of simulations spanning multiple time and length scales. This is possible by combining expensive small-scale simulations (such as molecular dynamics simulations) with larger scale simulations (such...

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive m...

Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh elements. For instance, quantitative predictions of transport in nanoporous media, critical to hydrocarbon extrac...

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive m...

The Exascale Computing Project (ECP) is invested in co-design to assure that key applications are ready for exascale computing. Within ECP, the Co-design Center for Particle Applications (CoPA) is addressing challenges faced by particle-based applications across four sub-motifs: short-range particle-particle interactions (e.g., those which often do...

The Exascale Computing Project (ECP) is invested in co-design to assure that key applications are ready for exascale computing. Within ECP, the Co-design Center for Particle Applications (CoPA) is addressing challenges faced by particle-based applications across four “sub-motifs”: short-range particle–particle interactions (e.g., those which often...

We discuss the implementation of a finite element method, used to numerically solve the Euler equations of compressible flows, using an asynchronous runtime system (RTS). The algorithm is implemented for distributed-memory machines, using stationary unstructured 3D meshes, combining data-, and task-parallelism on top of the Charm++ RTS. Charm++’s e...

Plasma flows encountered in high-energy-density experiments display features that differ from those of equilibrium systems. Nonequilibrium approaches such as kinetic theory (KT) capture many, if not all, of these phenomena. However, KT requires closure information, which can be computed from microscale simulations and communicated to KT. We present...

Fine-scale models that represent first-principles physics are challenging to represent at larger scales of interest in many application areas. In nanoporous media such as tight-shale formations, where the typical pore size is less than 50 nm, confinement effects play a significant role in how fluids behave. At these scales, fluids are under confine...

We present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green’s function theory in the GW approximation with the Bethe–Salpeter equation (BSE). This work provides a summary of the underlying theory and discusses the details of its implementation based on Gaussian orbit...

div>We present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green’s functions theory in the GW approximation with the Bethe–Salpeter Equation (BSE). This work provides a summary of the underlying theory and discusses details of its implementation based on Gaussian orbi...

Molecular simulation is a scientific tool used in many fields including material science and biology. This requires constant development and enhancement of algorithms within molecular simulation software packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the...

Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identify techniques, the code...

Parallel trajectory splicing, or ParSplice, is an attempt to solve the enduring challenge of simulating the evolution of complex atomistic systems over long time scales. • Conventional molecular dynamics (MD) suffer from time scale limitations. • Typical simulations can only be performed for durations on the order of nanoseconds. • Hinders physical...

We investigate the role of the thermodynamic (TD) force as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution molecular dynamics setup assures thermodynamic equilibrium between atomistically resolved and coarse-grained re...

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the l...

We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-gr...

LA-UR-18-20754
Concept-based runtime polymorphism with Charm++ chare arrays using value semantics
We discuss a generic and migratable C++ helper class that enables runtime polymorphism among chare arrays using value semantics. This enables hiding, behind a single type, different Charm++ array proxy types that model a single concept, i.e., define...

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those met...

Talk given at http://charm.cs.illinois.edu/workshops/charmWorkshop2017

We discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within 10%–15% accuracy, is given by the Amdahl’s Law adapted to the specific quantities involved in the problem. Th...

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, t...

Multiscale physics applications present an interesting problem from a computer science standpoint as task granularity has the potential to vary drastically which places a heavy burden upon the task scheduler and load balancer. Additionally, due to the long execution time of some of these computations, fault tolerance becomes a necessity as not bein...

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both met...

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software-hardware co-design choices relevant to scientific applications and hardware architectures. We present a new class of tools called application simulators-parameterized fast-running proxies of large-scale scientific app...

We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the origin...

We describe the adaptive resolution multiscale method AdResS. The conceptual
evolution as well as the improvements of its technical efficiency are described
step by step, with an explicit reference to current limitations and open
problems.

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, for example, all-atom, to low, that is, coarse-grained, resolution. Using...

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.

We show direct formal relationship between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work-horses for sampling from a generalized, multicanonical ensemble. We demonstrate that statistical te...

For the example of C60 solutes in toluene, we present the implementation of the adaptive resolutions scheme (AdResS) for molecular simulations into GROMACS. In AdResS a local, typically all-atom cavity is coupled to a surrounding of coarse-grained, simplified molecules. This methodology can not only be used to reduce the CPU time demand of atomisti...

We present a multiresolution simulation scheme for the solvent environment where four atomistic water molecules are mapped onto one coarse-grained bead. Soft restraining potentials are used to allow a resolution exchange of four water molecules into a single coarse-grained site. We first study the effect of adding restraining potentials in liquid w...

We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the othe...

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an inter...

We present an approach to systematically coarse-grain liquid mixtures using the fluctuation solution theory of Kirkwood and Buff in conjunction with the iterative Boltzmann inversion method. The approach preserves both the liquid structure at pair level and the dependence of solvation free energies on solvent composition within a unified coarse-gra...

Biological organizations depend on a sensitive balance of noncovalent
interactions, in particular also those involving interactions of small
molecules, including inorganic salts and urea, with biomolecules in
aqueous solution. Computer simulations of these types of systems require
simple-yet-specific models in order to cover all relevant time and
l...

Gentoo ist die etwas andere Linux-Distribution: Anwender installieren Softwarepakete aus den Quelltexten, die Programme werden permanent auf dem aktuellen Stand gehalten. Dank einer ausgefuchsten Paketverwaltung ist das erstaunlich einfach.

Several systematic coarse-graining techniques have been developed in recent years. The method of choice depends on the system of interest and the properties to be reproduced. We present three hybrid schemes to combine force-matching and Boltzmann inversion. The methods are tested on liquid hexane and the results are compared to iterative Boltzmann...

We discuss the hierarchy of subphase transitions in first-order-like
nucleation processes for an exemplified aggregation transition of
heteropolymers. We perform an analysis of the microcanonical entropy, i.e., the
density of states is considered as the central statistical system quantity
since it connects system-specific entropic and energetic inf...

By means of multicanonical computer simulations, we investigate thermodynamic
properties of the aggregation of interacting semiflexible polymers. We analyze
a mesoscopic bead-stick model, where nonbonded monomers interact via
Lennard-Jones forces. Aggregation turns out to be a process, in which the
constituents experience strong structural fluctuat...

The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting th...

We review the adaptive resolution scheme (AdResS) from a technical perspective and collect arguments from several years of research, which culminates into the implementation of AdResS into the open-source package ESPResSo. This flexible implementation allows us to repeat all previous AdResS simulations with one program. We test this reference imple...

Convective turbulence with phase changes and latent release is an important dynamical process in the atmosphere of the Earth which causes, e.g. the formation of clouds. Here we study moist convection in a simplified setting – shallow and nonprecipitating moist Rayleigh-Bénard convection with a piecewise linear thermodynamics on both sides of the ph...

Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. Several coarse-graining techniques have so far been developed, such as iterative Boltzmann inversion, force-matching, and inverse Monte Carlo. However, there is no unified framework that implements these methods and that allows their...

We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geo...

The Adaptive Resolution Scheme (AdResS) is a simulation method, which allows to perform Molecular Dynamics (MD) simulations treating different regions with different molecular resolutions. The different scales are coupled within a unified approach by changing the number of degrees of freedom on the fly and preserving the free exchange of particles...

The relation between atomistic structure, architecture, molecular weight and material properties is a basic concern of modern soft material science. This by now goes far beyond standard properties of bulk materials. A typical additional focus is on surface or interface aspects or on the relation between structure and function in nanoscopic molecula...

We employ a mesoscopic model for studying aggregation processes of proteinlike hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to non-negligible surface...

We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase transition in the thermodynamic sense, the observed folding-binding behavior exhibits fascinating features leadin...

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the adv...

We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase transition in the thermodynamic sense, the observed folding-binding behavior exhibits fascinating features leadin...

We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite length, we find that the microcanonical entropy behaves convex in the transition region, leading to a negativ...

We compare the efficiency of two prominent techniques for simulation of complex sys-tems: parallel tempering and Wang–Landau sampling. We show that both methods are of comparable efficiency but are optimized for different platforms. Parallel tempering should be chosen on multi-processor system while Wang–Landau sampling is easier to implement on a...

The aim of this work is to study the behavior of three advanced Monte Carlo methods in protein simulations employing a realistic ECEPP/3-based all-atom model . The implementation is based on the open source package SMMP4. The techniques applied were Wang-Landau sampling , parallel tempering and random tempering. All three techniques show very good...

## Projects

Projects (2)

Our goal is to simulate large and complex engineering multiphysics problems with a production-quality code that is extensible and maintainable, using hardware resources efficiently, even for problems with a priori unknown, heterogeneous, and dynamic load distribution.
For more details see https://quinoacomputing.org.