Related papers: Directly measuring single molecule heterogeneity u…
Force distance curves (FCs) are among the most direct measurements performed in atomic force microscopy (AFM), yet their information content is often reduced by filtering and quasi-static interpretation. Here, enabled by a new…
We perform extensive Molecular Dynamics simulations of an ensemble of realistic microgel particles in swollen conditions in a wide range of packing fractions $\zeta$. We compare neutral and charged microgels, where we consider charges…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Single-molecule F\"orster Resonance Energy Transfer (smFRET) is ideally suited to resolve the dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly…
Atomically-resolved imaging and force measurements using the atomic force microscope (AFM) are performed most commonly in a frequency-modulation (FM) mode. This has led to spectacular results, including direct observation of the atomic…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
We study the influence of cell-level mechanical heterogeneity in epithelial tissues using a vertex-based model. Heterogeneity in single cell stiffness is introduced as a quenched random variable in the preferred shape index($p_0$) for each…
The use of probe molecules to extract the local dynamical and structural properties of complex dynamical systems is an age-old technique both in simulations and experiments. A lot of important information which is not immediately accessible…
For defining the conductance of single molecule junctions with a redox functionality in an electrochemical cell, two conceptually different electron transport mechanisms, namely coherent tunnelling and vibrationally induced hopping compete…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
Clarifying electronic and vibronic properties at individual molecule level provides key insights to future chemistry, nanoelectronics, and quantum information technologies. The single electron tunneling spectroscopy has been used to study…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
The forced rupture of single chemical bonds under external load is addressed. A general framework is put forward to optimally utilize the experimentally observed rupture force data for estimating the parameters of a theoretical model. As an…
Accurate assessment of stiffness distribution is essential due to the critical role of single cell mechanobiology in the regulation of many vital cellular processes such as proliferation, adhesion, migration, and motility. Cell stiffness is…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Roughness parameters that characterize contacting surfaces with regard to friction and wear are commonly stated without uncertainties, or with an uncertainty only taking into account a very limited amount of aspects such as repeatability of…
Single-file transport, arising in quasi one-dimensional geometries where particles cannot pass each other, is characterized by the anomalous dynamics of a probe, notably its response to an external force. In these systems, the motion of…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…