Johannes Josef Schneider

• ZHAW Zurich University of Applied Sciences

Engineered artificial cells often involve phospholipid membranes in the form of vesicles or membrane mimics. Droplet interface bilayers (DIBs) constitute a commonly used membrane mimic within synthetic biology. However, these model membranes have limited accessibility due to their requirement to be surrounded by an oil environment. Here, we demonst...

We simulate the movement and agglomeration of oil droplets in water under constraints, using a simplified stochastic-hydrodynamic model. We analyze both local and global properties of the networks formed by the agglomerations of droplets for various system sizes. We focus on the differences of these properties for monodisperse and polydisperse syst...

Experimentally, periodically released droplets in systems of widening pipes show clustering. This is surprising, as purely hydrodynamic interactions are repulsive so that agglomeration should be prevented. In the main part of this paper, we investigate the clustering of droplets under the influence of phenomenological hydrostatic forces and some hy...

Within the scope of the European Horizon 2020 project ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function, we aim at the development of a chemical compiler governing the three-dimensional arrangement of droplets, which are filled with various chemicals. Neighboring droplets form bilayers with pores which allow chemicals to m...

We present some work in progress on the development of a probabilistic chemical compiler, being able to make a plan of how to create a three-dimensional agglomeration of artificial hierarchical cellular constructs. Such programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory being able to pr...

We aim at planning and creating specific agglomerations of droplets to study synergic communication using these as programmable units. In this paper, we give an overview of preliminary obstacles for the various research issues, namely of how to create droplets, how to set up droplet agglomerations using DNA technology, how to prepare them for confo...

The development of data science, the increase of computational power, the availability of the internet infrastructure for data exchange and the urgency for an understanding of complex systems require a responsible and ethical use of computational models in science, communication and decision-making. Starting with a discussion of the width of differ...

Within the scope of the European Horizon 2020 project ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function, we aim at the development of a chemical compiler governing the three-dimensional arrangement of droplets, which are filled with various chemicals. Neighboring droplets form bilayers containing pores through which chemic...

In this publication, the model by Ramsey, Pierce, and Bowman for finding the hierarchical order of the various sectors of an economy, conceiving each of them as users or suppliers for other sectors of the economy, is investigated. Computational results for a benchmark instance are provided.KeywordsSimulated annealingThreshold acceptingRamseySpin gl...

We explain how to optimize the image analysis of mixed clusters of red and green droplets in solvents with various degrees of sharpness, brightness, contrast and density. The circular Hough Transform is highly efficient for separated circles with reasonable background contrast, but not for large amounts of partially overlapping shapes, some of them...

We present some work in progress on the development of a probabilistic chemical compiler, being able to make a plan of how to create a three-dimensional agglomeration of artificial hierarchical cellular constructs. These programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory being able to e...

We provide a practical construction to map (slightly modified) GOTO-programs to chemical reaction systems. While the embedding reveals that a certain small fragment of the chemtainer calculus is already Turing complete, the main goal of our ongoing research is to exploit the fact that we can translate arbitrary control-flow into real chemical syste...

We present some work in progress on the development of a small portable biochemical laboratory, in which spatially structured chemical reaction chains in a microfluidic setting shall be created on demand. For this purpose, hierarchical three-dimensional agglomerations of artificial cellular constructs are generated which will allow for a governed g...

For a few years, Simulated Annealing (SA)1 and related Monte Carlo optimization algorithms like Threshold Accepting (TA)2 have become a useful means for optimizing various kinds of economic problems, like the Traveling Salesman Problem (TSP). In this paper, we concentrate on the production processes themselves because most costs are thereby incurre...

Search space smoothing and related heuristic optimization algorithms provide an alternative approach to simulated annealing and its variants: while simulated annealing traverses barriers in the energy landscape at finite temperatures, search space smoothing intends to remove these barriers, so that a greedy algorithm is sufficient to find the globa...

For an intriguing variety of switching processes in nature, the underlying complex system abruptly changes from one state to another in a highly discontinuous fashion. Financial market fluctuations are characterized by many abrupt switchings creating upward trends and downward trends, on time scales ranging from macroscopic trends persisting for hu...

Simulated annealing is the classic physical optimization algorithm, which has been applied to a large variety of problems for many years. Over time, several adaptive mechanisms for decreasing the temperature and thus controlling the acceptance of deteriorations have been developed, based on the measurement of the mean value and the variance of the...

In the original traveling salesman problem, the traveling salesman has the task to find the shortest closed tour through a proposed set of nodes, touching each node exactly once and returning to the initial node at the end. For the sake of the tour length to be minimized, nodes close to each other might not be visited one after the other but separa...

Some years ago, Bachem, Hochstättler, and Malich proposed a heuristic algorithm called Simulated Trading for the optimization of vehicle routing problems. Computational agents place buy-orders and sell-orders for customers to be handled at a virtual financial market, the prices of the orders depending on the costs of inserting the customer in the t...

For many years, the problem of how to distribute students to the various universities in Germany according to the preferences of the students has remained unsolved. Various approaches, like the centralized method to let a central agency organize the distribution to the various universities or the decentralized method to let the students apply direc...

The compute unified device architecture is an almost conventional programming approach for managing computations on a graphics processing unit (GPU) as a data-parallel computing device. With a maximum number of 240 cores in combination with a high memory bandwidth, a recent GPU offers resources for computational physics. We apply this technology to...

The compute unified device architecture (CUDA) is a programming approach for performing scientific calculations on a graphics processing unit (GPU) as a data-parallel computing device. The programming interface allows to implement algorithms using extensions to standard C language. With continuously increased number of cores in combination with a h...

We consider the problem of finding the densest closed packing of hard disks with proposed different radii in a circular environment, such that the radius of the circumcircle is minimal. The subspace of the quasioptimum configurations of this problem exhibits the property of ultrametricity.

We consider the problem of finding the densest closed packing of hard disks with proposed different radii in a circular environment, such that the radius of the circumcircle is minimal. With our approach, we are able to find denser packings for various problem instances than known from the literature. Both for the dynamics of the simulation and for...

Our publication focuses on two different but related topics in politics: in the first part of this publication, we investigate the influence of election results in the elections for the parliaments of the German states and for the German Diet (federal parliament) on the member numbers of the largest parties in the various states. In the second part...

When trying to find approximate solutions for the Traveling Salesman Problem with heuristic optimization algorithms, small moves called Lin-k-Opts are often used. In our paper, we provide exact formulas for the numbers of possible tours into which a randomly chosen tour can be changed with a Lin-k-Opt. Furthermore, we compare the quality of the res...

We recently introduced a realistic order book model [T. Preis, Europhys. Lett. 75, 510 (2006)] which is able to generate the stylized facts of financial markets. We analyze this model in detail, explain the consequences of the use of different groups of traders, and focus on the foundation of a nontrivial Hurst exponent based on the introduction of...

When trying to find approximate solutions for the Traveling Salesman Problem with heuristic optimization algorithms, small moves called Lin-$k$-Opts are often used. In our paper, we provide exact formulas for the numbers of possible tours into which a randomly chosen tour can be changed with a Lin-$k$-Opt.

Envy is a rather complex and irrational emotion. In general, it is very difficult to obtain a measure of this feeling, but in an economical context envy becomes an observable which can be measured. When various individuals compare their possessions, envy arises due to the inequality of their different allocations of commodities and different prefer...

Envy is a rather complex and irrational emotion. In general, it is very difficult to obtain a measure of this feeling, but in an economical context envy becomes an observable which can be measured. When various individuals compare their possessions, envy arises due to the inequality of their different allocations of commodities and different prefer...

We investigate several variants of a network creation model: a group of agents builds up a network between them while trying to keep the costs of this network small. The cost function consists of two addends, namely (i) a constant amount for each edge an agent buys and (ii) the minimum number of hops it takes sending messages to other agents. Despi...

Since its introduction in 2000, the Sznajd model has been assumed to simulate a democratic community with two parties. The main flaw in this model is that a Sznajd system freezes in the long term in a non-democratic state, which can be either a dictatorship or a stalemate configuration. Here we show that the Sznajd model has better to be considered...

In the Sznajd model, a democratic community with two parties is simulated. A large drawback of this model is that it always ends up in non-democratic states. Here I give two examples how the additional introduction of contrarian and opportunistic behaviors of individuals can keep a democracy alive.

Simulated Annealing has become a standard optimization technique for a wide variety of problems: starting at a random configuration and performing a sequence of moves, the system is optimized using a control parameter which partially allows for accepting a deterioration and therefore for climbing over barriers in the energy landscape. Our approach,...

In this paper, we investigate the relations between the numbers of members of various parties and their results in the elections in Bavaria and in Germany. Deriving from the finding that there is a strong time-delayed correlation between these data-sets for the two largest parties in Bavaria, we show in a simulation based on the Sznajd model that s...

We investigate the lifetimes of governments in the original and a randomized one-dimensional Sznajd model. We find various scaling laws for the lifetime of the democracy and for the reigning time of governments in this model, depending on the system size N.

The classic distributed computation is done by atoms, molecules or spins in vast numbers, each equipped with nothing more than the knowledge of their immediate neighborhood and the rules of statistical mechanics. These agents, 1023 or more, are able to form liquids and solids from gases, realize extremely complex ordered states, such as liquid crys...

Sznajd-Weron and Sznajd introduced a model investigating the democratic development in a closed community. This model is based on the USDF-principle ("united we stand, divided we fall"). However, it faces the problem that the system tends either to a dic-tatorship (i.e., 100% pro or 100% contra) or to a stalemate state (i.e., exactly 50% pro, 50% c...

As the Nagel-Schreckenberg model (NaSch model) became known as a realistic approach to describe traffic flow on single-lane streets, this model was extended to two-lane traffic by several groups. On the base of our two-lane model, we will now investigate the impact of a place of obstruction, e.g., because of road works, on partial fractions, densit...

Comparing different good solutions for an optimization problem, one usually finds structures which are common to all solutions. Thus, one can assume that these ``backbones'' are part of any good solution and also of the global optimum of the considered problem. For spin glass models like the Sherrington-Kirkpatrick-model, these backbones consist of...

The Nagel–Schreckenberg-model (NaSch-model) describes macroscopic features of real traffic very well. However, the characterization of a single car driver's behavior in some details is not realistic, e.g., the NaSch-driver calculates his/her distance to the car in front from the position this car has just in the very moment and ignores that it coul...

During the last few years, simulated annealing and related Monte Carlo optimization algorithms such as threshold accepting have become a useful means for finding the ground states of complex physical problems and for optimizing various kinds of economic problems, such as the Traveling Salesman Problem (TSP). In this article, we show how these metho...

A problem often considered in operations research and computational physics is the traveling salesman problem, in which a traveling salesperson has to find the shortest closed tour between a certain set of cities. This problem has been extended to more realistic scenarios, e.g., the "real" traveling salesperson has to take rush hours into considera...

The Nagel–Schreckenberg model (NaSch model) proved to be a realistic approach to describe traffic flow on single-lane streets. In this paper, we add some lane changing rules for two-lane traffic and discuss the influence of the variation on the mean velocity and the flow.

A highly efficient parallel algorithm called Searching for Backbones (SfB) is pro- posed: based on the fact, that many parts of a good configuration for a given optimization problem are the same in all other good solutions, SfB reduces the complexity of this problem by finding these "backbones" and eliminating them in order to get even better solut...