Öffentliche Seminare

Ort: Digital see link
I will present techniques to find reaction coordinates to be used in conjunction with free energy biasing techniques such as the adaptive biasing force method. This allows for instance to improve the sampling of configurations of complex proteins. However, reaction coordinates are often based on an intuitive understanding of the system, and one would like to complement this intuition or even replace it with automated tools. One appealing tool is autoencoders, for which the bottleneck layer provides a low dimensional representation of high dimensional atomistic systems. I will discuss some mathematical foundations of this method, and present illustrative applications including alanine dipeptide. Some on-going extensions to more demanding systems, namely HSP90, will also be mentioned by Zineb Belkacemi, the PhD student working on this project. [mehr]

Dynamic Load Balancing for Parallel Particle Simulations

Parallel computing has developed as a central tool in scientific computing to solve large scale problems involving huge number of degrees of freedom, complex geometries or coupled applications. The parallel efficiency is key for estimating to which degree the computational resources are used, or whether there is still potential to speed up an application by organising data or workflow in a different way across processors. To reduce the wall clock time of an application, a goal might be to use as many processors of a parallel architecture as possible. However, scalability of a parallel application depends on a number of characteristics, among which is efficient communication, equal distribution of work or efficient data layout.Many parallel applications, especially particle or mesh based algorithms like Molecular Dynamics or Lattice Boltzmann methods, are implemented by domain decomposition techniques, where processors administrate certain geometrical regions of a physical system. In such cases, unequal work load in the processor network is to be expected when particles are not distributed homogeneously or the computation cost of particle interactions is not equal in each part of the system. Also in the case where heterogeneous architecture components are coupled together in a complex cluster network (e.g. CPU-GPU, different types of CPUs or different network speeds) wall clock times for solving a problem with the same number of degrees of freedom will vary across the parallel application. For these scenarios the code has to decide how to redistribute the work among processes according to a work sharing protocol or to dynamically adjust computational domains, to balance the workload.In the seminar, I will give an introduction to the problem of load balancing and discuss various methods to redistribute data or re-organise the domain decomposition to improve and optimise the work load and to improve parallel efficiency and scalability. As an outlook I will discuss developments from the European Centre of Excellence E-CAM, where different methods have been implemented into a library, which can be used in community codes. [mehr]

Taming complex fluids with thermal fields

External fields, thermal and electromagnetic, induce a range of non-equilibrium effects in complex fluids consisting of nanoparticle suspensions (Soret, Seebeck, Peltier effects), which can be exploited in energy conversion (thermoelectrics), analytical devices for detection of biomolecules, or nanoparticle transport and assembly. The combination of Non-Equilibrium multiscale simulations and theory has paved the way to explain the physical behaviour of complex fluids under external fields, showing that their response is much richer than previously predicted. I will discuss how simulation techniques can be used to obtain thermophysical properties relevant in energy conversion problems and to uncover novel non-equilibrium effects in complex fluids, associated to the coupling of internal degrees of freedom of molecules and colloids with thermal fields. [mehr]

Dynamics of Soft Matter in Increasingly Complex Environments

Recent advancements in the understanding of the dynamics of soft matter is presented, concentrating on polymer melts with some outlook on semiconducting polymers and lipid membranes in solution. Traditionally, techniques like rheology are very popular, as these enable high-throughput experiments that help connect model materials with applications. Despite substantial progress, even the simplest model materials are not entirely understood, at least when it comes to a simultaneous modeling of experimental results from different techniques. This indicates that there is still a lack of information that prevents holistic understanding. This presentation concentrates on augmented analysis of recent experimental results on bottlebrush polymer melts, semiconducting polymers in solutions, and lipid membranes. Using the advantage of length- and time-scale dependent information of neutron spectroscopy, we distinguish different processes in polymer melts, nanocomposites, bottlebrushes, semiconducting polymers, and lipid membranes. As the results point to a generic picture, the procedures used appear to be a promising path to further elevate fundamental understanding of polymers, including confined chains and architectures of increasing complexity. [mehr]

Improving accuracy of systematic coarse-grained simulations

Billion atom simulations are just now becoming possible in molecular simulation for nanoseconds. We've also crossed the millisecond barrier for simulating biomacromolecules. What's left? Unfortunately, a typical cell contains 100 trillion atoms. Even simulating something like a polymer nanoparticle (~100 million atoms) has timescales of interest far beyond nanoseconds. One way around the length-scale limitation is coarse-grained simulation. Coarse-graining requires two ingredients: (i) a mapping that determines how to group atoms into coarse beads and (ii) a force field that describes these interactions. In this talk, I will describe our recent progress on determining mapping operators, which has previously been an arcane topic with little rigor. We've developed novel theory, shown what role symmetry plays, and developed ML models that find mappings for arbitrary molecular systems. Finding the force field of a coarse-grained model is a rich field with a long history. Typically, it is broken into two types: top-down, where we choose the force field to reproduce an observed phonemenon in experiment; and bottom-up, where we draw upon the observed forces in a molecular simulation. I will describe our recent work on combining these approaches to create hybrid top-down/bottom-up models via the principle of maximum entropy. [mehr]

Understanding the friction of atomically thin layered materials

Friction is a ubiquitous phenomenon that greatly affects our everyday lives and is responsible for large amounts of energy loss in industrialised societies. Layered materials such as graphene have interesting frictional properties and are often used as (additives to) lubricants to reduce friction and protect against wear. Experimental Atomic Force Microscopy studies and detailed simulations have shown a number of intriguing effects such as friction strengthening and dependence of friction on the number of layers covering a surface. Here, we propose a simple, fundamental, model for friction on thin sheets. We use our model to explain a variety of seemingly contradictory experimental as well as numerical results. This model can serve as a basis for understanding friction on thin sheets, and opens up new possibilities for ultimately controlling their friction and wear protection. [mehr]
Amyloid fibrils are well-ordered supramolecular polymers consisting of thousands of protein molecules connected via intermolecular hydrogen bonds. For intrinsically disordered proteins (IDP), amyloid form is thermodynamically more stable than the native form, and its formation in human body can lead to pathology. Namely, misfolding of small intrinsically disordered neuronal protein α-synuiclein is a hallmark of Parkinson's disease. The fibrillization is an autocatalytic process that can be induced by small amounts of pathological fibrils in a prion-like manner. We studied detailed kinetic mechanism of the α-synuiclein fibrillization and have shown that atypical sigmoidal reaction kinetics and exponential distribution of the length of formed fibrils are the results of a two-step autocatalytic cycle that includes fibril elongation via binding monomers to the ends and formation of new fibril ends due to fibril breaking [1]. This allowed us to identify the fibril ends as the bottleneck of the process and thus the most prospective target for fibrillization inhibitors. We designed several proteins and peptides that selectively bind to the fibril ends and block their growth by creating a steric hindrance [2,3]. This approach permits inhibition of fibril formation at inhibitor concentrations orders of magnitude lower than the concentration of monomeric α-synuclein. In my talk, I will focus mostly on the application of mathematical models for determination of the reaction mechanism based on kinetic data and on design of experiments for refining the models and proving the mechanism. [mehr]

Conducting polymers and bioinspired materials for organic bioelectronics

Organic electrochemical transistors (OECTs) have rapidly surged as amplifying transducers forbiosensing or diagnostic devices and for cells/nerves stimulation. 1 OECTs translate ionic signalsinto electric current using an electrolyte in direct contact with a conducting polymer channel.Unlike in organic field effect transistors where charge transport involves only a small layer, ionsin OECTs permeate the entire volume of the active material. This results in devices having highersignal amplification and lower operating voltage. 1 At the heart of OECTs working principle is theorganic mixed ionic-electronic conductor, usually a π- conjugated polymer (or polymer blend)able to host (or chemically linked to) charged groups.The greatest challenge of developing high-performing mixed conductors is optimizing theseemingly conflicting processes of electronic and ionic charge transport. 2 The chemical featuresof mixed conductors make them hydrophilic; however, little is known about how water and ionsaffect their microstructure and charge transport, as well as their long-term operational stabilityand biocompatibility.A successful strategy towards suitable materials for OECTs is to modify conducting polymerssuch as polythiophenes to make them hydrophilic, using glycolated substituents. 3 I am currentlyinvestigating the role of glycolated side chains in ion coordination and polymer morphology, 4,5and developing a methodology to describe swelling and morphology changes upon ionpenetration and doping in these materials.A different path towards new bioelectronic materials is to instead use natural mixed conductingpolymers that are intrinsically biocompatible, either alone or in composites. Synthetic polymersderiving from eumelanin (the black pigment in our skin, hair and eyes) are promisingbiocompatible, non-cytotoxic components in OECTs or other optoelectronic devices: 6-8 theyfeature both electronic and protonic charge carriers, can be prepared in large batches undercontrolled conditions, and easily incorporated into hybrid materials.I am currently studying the structure, self-assembly and electronic properties of eumelanin-derived materials. My model takes into account the chemical disorder of eumelanin(tautomerisation, oxidation and proton exchange sites) and aims to elucidate its effect on theelectronic structure and charge transport characteristics of this material. In particular, I aminvestigating the peculiar dipole-dependent properties of DHICA melanin 9 and itssupramolecular organisation; this rigid polymer can be spun into fibers with promisingmechanical and charge transport properties. [mehr]
The invention of new materials combined with an improved knowledge of structure-property relationships of organic donor-acceptor blends led to an impressive improvement in their energy conversion efficiency to 17 % [1]. This success seems to contradict the simple view that the long range Coulomb interaction between electrons and holes in organic semiconductors causes inefficient formation but efficient recombination of free charge. An important characteristic of organic solar cells is that they comprise at least two organic components of different chemical structure, introducing a large complexity of the morphology and electron landscape of the active layer. In this talk, I will present results regarding the generation and recombination of free charges in selected bulk heterojunction solar cells, with particular focus on the role of the interfacial CT state. We show that free charge formation proceeds predominately through low energy CT states, ruling out the predominance of a hot CT dissociation pathway, and that the same states dominate the subsequent recombination [2]. For fullerene-based solar cells with a low donor content, we find that the efficiency of charge generation is limited by the same mechanism that limits the VOC, namely non-radiative recombination of the CT states via vibronic coupling [3]. Notably, the rate of this recombination process obeys the classical energy gap law, implying that donor-acceptor blends benefit from a higher CT energy through longer CT lifetimes and more efficient photocurrent generation [4]. Consistent with this result, we observe that devices suffer from inefficient CT dissociation also through a higher rate of non-geminate recombination [5]. As a consequence, it’s only the systems with very efficient charge generation and very fast CT dissociation that the free carrier recombination is strongly suppressed, irrespective of the details of the spin statistics. We, finally, present recent results on a highly efficient polymer:NFA blend, where we find a surprisingly low activation energy for free charge generation, despite a low energy offset at the heterojunction [6]. These results highlight the importance of a comprehensive understanding of the energy landscape, and how it affects the pathway from the bound CT exciton to the spatially separated electron-hole pair. [mehr]
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