Filtyp
We present a method based on CRISPR/Cas9 excision and DNA combing to detect anti-microbial resistance (AMR) genes on bacterial plasmids. The assay is inexpensive, simple, fast, and also provides information on the number and size of plasmids in a sample. We demonstrate detection of the gene encoding for the New Delhi metallobeta-lactamase 1 (blaNDM-1) enzyme, known to make bacteria resistant to a
The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level
The 16 - 22 amino-acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta(16-22) peptides by unbiased thermodynamic simulations at the atomic level for systems of one, three, and six Abeta(16-22) peptides. We find that the isolated Abeta(16-22) peptide is mainly a random coil i
A third workshop on small-x physics, within the Small-x Collaboration, was held in Hamburg in May 2004 with the aim of overviewing recent theoretical progress in this area and summarizing the experimental status.
We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is abl
Divergent-light halos are produced when light from nearby light sources is scattered by ice crystals in the atmosphere. We present a theory of divergent-light halos leading to an improved algorithm for the simulation of such halos. Contrary to the algorithm that we presented earlier for simulating such halos, the new algorithm includes a mathematically rigorous weighting of the events. The compute
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with; 20 residues each. The test set contains both alpha-helical ( Trp cage, F-s) and beta-sheet ( GB1p, GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely sequence-based, is able to fold these different peptides for one and the same choice of model param
This paper proposes and investigates a Bayesian relation between optimal L2 regularization strengths and the number of training patterns and hidden nodes used for an artificial neural network. The results support the proposed dependence for number of training patterns, while the dependence on hidden architecture was less clear. Finally, applying different regularization strengths on different laye
Fitting a model to a time-dependent ensemble average is a process repeated frequently throughout biophysics. A selected ensemble-averaged observable (⟨y(t)⟩) for a given system can be predicted through the use of an estimated ensemble average, where the estimated ensemble average is created via simulated or experimental data sets. Fitting a model to this estimated ensemble average allows for estim
Previously, Berg and Purcell found an expression for the diffusion current of particles into a set of receptors in their paper Physics of Chemoreception. These receptors were assumed to be uniformly distributed on a spherical cell's surface and the receptors where idealized as circular patches. For their model, the particles' diffusion constant was the same for all points outside of the ce
This thesis examines the state-of-the-art 2D super-resolution technique alternating descent conditional gradient (ADCG) method's ability to accurately localize fluorophores in diffraction-limited single molecule images (SMI) and analyze the impact of pre-processing and post-processing modules on ADCG's fluorophore localization. A synthetic dataset obtained from the 2013 Grand Challenge loc
DNA barcodes carry coarse-grained genetic information of DNA sequences taken from a genome. Potential applications include bacteriology, medical diagnosis and taxonomy. However, the current state-of-the-art tools for extracting DNA molecules from cells provide only fragmented pieces of chromosomal DNA. As a consequence, also DNA barcodes are fragmented. This calls for the development of complement
Neurodegenerative diseases such as Parkinson’s can be treated with stem-cell derived specialized neurons. In order to achieve precise directed neural differentiation in vitro we need to understand the gene regulatory mechanisms behind in vivo neural tube patterning. We implement a 3D computational model of brain patterning to simulate this process. The mathematical model is set up by unifying two e
In the field of computational biology, fluorescence microscopy images often constitute the input source of information. The process of binarization of raw images to delineate interesting objects requires image segmentation into signal and background pixels. Several methods to perform image segmentation exist, the Otsu method being a popular unsupervised example. The Otsu method's lack of pro
Amino acids that are in close contact in a protein structure tend to co-evolve, which gives rise to sequence correlations. Direct coupling analysis (DCA) is a method for predicting such contacts directly from sequence correlations, without assuming any prior knowledge of structures. To this end, sequence correlations are modeled using an Ising-like ansatz, whose couplings are determined through an
Convolutional Neural Networks (CNNs) and pre-trained word embeddings have revolutionized the field of Natural Language Processing (NLP) during the last years. In this project, CNNs are used on top of the Word2Vec word representation for a sentence classification task on medical research articles. Both individual networks for each category as well as a combined classification network are optimized
During the last few years, crowding effects on the physics of proteins has become an increasingly popular topic of research. This is is because most biological processes involving proteins naturally take place in a crowded environment, e.g. in the cellular environment where macromolecules may occupy 30% of the volume. One such biological process would be the formation of amyloid aggregates, which
