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Algorithms for Long Range Interactions

A potential is defined to be short ranged if it decreases with distance $r$ quicker or similar than $r^{-(d-1)}$ where $d$ is the dimensionality of the system. Electrostatic, gravitatory and dipolar interactions, present in many physical systems, are examples of long range interactions. When long range intgeractions are present in a system, the weight of the interactions comming from far particles is non negligible. more...

Capillarity in Porous Media

Capillarity in Porous Media more...

DNA Electrophoresis

Electrophoresis is one of the main techniques to separate DNA molecules by size and has shown its effectiveness in the sequencing of entire genomes, including our own. This success story also increased the demand for improved and faster sequencing methods, in order to meet the upcoming challenges. more...

ESPResSo

ESPResSo is a free, open-source software package for simulations of soft-matter systems, which is co-developed and used in the working group for most of its research. more...

Electrohydrodynamics

Many new and exciting physical phenomena occur in charged systems in solution, where the interplay between the hydrodynamic forces and the electrostatic interaction plays an important role in determining the dynamical properties.

Using ESPResSo we are investigating many different systems, especially in confined geometries, like the transport properties of ionic solutions in nanopores during DNA translocation, electro-osmotic flow in slit pores and properties of suspensions of confined charged colloids, in particular in slit and cylindrical pores. more...

Ferrofluids

Dipolar magnetic fluids (also known as ferrofluids or ferrocolloids), are colloidal suspensions of ferromagnetic nanoparticles (typical sizes 10-20nm), usually stabilised by steric coatings (in non electrolyte carrier liquids) or by electrical double layers (in aqueous solutions). Sterical coatings are usualy made of a stabilizing dispersing agent (surfactant) which prevents particle agglomeration even when a strong magnetic field gradient is applied to the ferrofluid. more...

GPU Computing

In the last couple of years, the computational power of graphics cards has grown much faster than that of conventional CPUs, although at the same time the graphics cards have become true general purpose processors. Recent graphics processors reach speeds of up to a Teraflop on a single PCIe-board. With the introduction of easy-to-use programming languages for the GPU hardware, this computational power can be harnessed for many applications. We use GPU computing to accelerate our computer simulations. more...

Ionic Liquids

Ionic Liquids (ILs) are a subclass of molten salts which

have a melting point below 100°C. ILs have been known for more than 90 years, however, recently found members of this class have shown promise in applications in electrochemistry, analytics, technology, and engineered fluids. Many ILs are liquid at room temperature, with some freezing at temperatures around -90°C. Due to their salt like structure they usually exhibit a negligible vapor pressure up to high temperatures, making them particularly suited for "green chemistry". IL's also exhibit interesting solvation or coordination properties, suggesting that one could potentially use them as "designer solvents". more...

Multiphase Flow in Porous Media

Many natural and technical processes involve multiphase flow

processes in porous media. Despite that fact fundamental concepts of twophase flow on macroscopic scales still remain unclear. The predictive power of the most commonly used extended multiphase Darcy theory is at best limited to simple problems where neither hysteresis nor dynamic effects like trapping nor varying residual saturations have a substantial impact on the solutions. more...

Nanopore Sequencing

Translocation of peptides through an aerolysin nanopore. Taken from https://doi.org/10.1038/s41587-019-0345-2

Biologische Makromoleküle erfüllen lebenswichtige Aufgaben im menschlichen Körper. Als Energielieferanten, Stoffwechselakteure, Bioroboter oder Signalbotschafter zwischen den Organen und für viele andere Stoffwechselvorgänge sind sie essentiell. Umso wichtiger ist die Erforschung deren Wirkungen und Strukturen, um beispielsweise Krankheiten besser zu verstehen und die genaue Wirkungsweise und Entwicklung von Medikamenten zu optimieren.

Biologische Makromoleküle erfüllen lebenswichtige Aufgaben im menschlichen Körper. Als Energielieferanten, Stoffwechselakteure, Bioroboter oder Signalbotschafter zwischen den Organen und für viele andere Stoffwechselvorgänge sind sie essentiell. Umso wichtiger ist die Erforschung deren Wirkungen und Strukturen, um beispielsweise Krankheiten besser zu verstehen und die genaue Wirkungsweise und Entwicklung von Medikamenten zu optimieren.

In der letzten Dekade ist es Forschern gelungen, eine effiziente und kostengünstige Methode zu entwickeln, um die Bausteine der DNA und RNA mit einzel-molekularer Auflösung und höchster Genauigkeit zu sequenzieren. Auf diesem Meilenstein aufbauend setzt sich das Zukunfstcluster nanodiag BW zum Ziel, diese Methodik der Makromolekülsequenzierung auf Proteine und Peptide zu erweitern.

Bei dieser Technik befindet sich das Analyt in einer Salzlösung, welche durch eine impermeable Lipid-Membran-Schicht getrennt ist. Diese Membran besitzt weiterhin eine Nanopore, die die zwei getrennten Hälften miteinander verbindet und somit die einzige Transportmöglichkeit von Atomen, Ionen und Molekülen auf die jeweils andere Seite darstellt. Eine extern angelegte elektrische Spannung führt nun zu einem elektrophoresischen Transport von Ionen und Analyt. Die Präsenz des Analyts in der Nanopore hat aufgrund verschiedenster atomistischer Wechselwirkungen mit allen möglichen Beteiligten schließlich eine temporäre Reduzierung des Leerstroms zur Folge, also des Ionenflusses unter der Abwesenheit jeglicher zu untersuchender Moleküle.

Anwendung von ML-Methoden

Aus der Information der Dauer und Stärke dieses sogenannten Blockadenstroms soll mithilfe modernster Machine Learning Algorithmen auf die Sequenzierung des zu untersuchenden Proteins oder Peptids geschlossen werden. Dabei werden experimentell bestimmte Sequenzierungsdaten analysiert, um auf unterschiedliche Analyte zurückführende Merkmale zu identifizieren. Als Teil des nanodiag BW Clusters ist unser Ziel die Erstellung einer Software, welche die Trainingsdaten lädt, sorgfältig analysiert und hervorstechende Merkmale extrahiert, um eine reproduzierbare und transparente Datenauswertung zu ermöglichen.

All-Atom und Multiskalensimulationen

Um die Auswirkungen des Analyttransports auf den Ionenstrom auf atomarer Ebene zu verstehen, führen wir molekulardynamische und Multiskalensimulationen der Peptid-Poreninteraktion durch. Die gewonnenen Erkenntnisse sollen der Optimierung der Porenproteine dienen, die schließlich qualitativ hochwertigere Messergebnisse ermöglichen.

Black Forest Nanopore Meeting

During the Black Forest Nanopore Meeting, we present a poster titled "Using Molecular Dynamics Simulation as a Microscope of the Peptide's Translocation Process through an Aerolysin Nanopore", where we show the latest results of the SRASKYRRRR peptide translocation through a wild-type aerolysin pore. An example of such a translocation is shown in the video below, which can be downloaded and viewed on your smartphone and other devices.

File:SRASKYRRRR translocation.avi

Kontakt

Für Fragen bezüglich der molekulardynamischen Simulationen steht ihnen Michel Mom (mmom(at)icp.uni-stuttgart.de) zur Verfügung. Unser Ansprechpartner für Fragen zum Thema Machine Learning ist Julian Hoßbach (jhossbach(at)icp.uni-stuttgart.de). more...

Nucleation in charged systems

The crystallization of charged macromolecules has a number of important applications in many fields, such as biology, pharmacology or materials design. For example, proteins are crystallized for purification or structure determination and colloidal crystals are promising candidates for photonic crystals. more...

Polyelectrolyte Multilayers

PEMs are composed of alternating layers of oppositely charged polyelectrolytes (PEs) (synthetic PEs or biomolecules), which are generally built up based on the Layer-by-Layer technique. [1,2] Due to their potential applications as membrane, encapsulation and matrix materials, and for enzymes and proteins in sensor applications, PEMs have stimulated great interests from both academic researchers and industries.[3] See also a PEM website. Despite the large number of experimental works, theoretical and computational studies toward understanding the microscopic structure of PEMs are scarce.[4]

more...

Transport in Porous Media

Understanding fluid transport in natural porous media is important for many

industrial and scientific applications. Computer simulations require accurate three-dimensional microscopic structure data as input and efficient numerical algorithms for fluid flow simulations. Natural porous media such as carbonates and clay filled sandstones exhibit heterogeneities on many scales and cannot be modeled by existing modeling techniques. more...

Understanding Single Molecule Experiments

Single molecule experiments (SME) have provided tools in high enough sensitivity and precision to manipulate, visualize and measure microscopic forces on individual molecules. Among many other SME techniques, Optical tweezers are particularly well suited to study polymer channel interactions (a nano-scale pore, biological or synthetic) and chain entropy. more...