Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.Comment: 25 pages, 1 table, 7 figures; preprint submitted to Biophysical Journa

High Conductance Ratio in Molecular Optical Switching of Functionalized Nanoparticle Self-Assembled Nanodevices

Self-assembled functionalized nano particles are at the focus of a number of potential applications, in particular for molecular scale electronics devices. Here we perform experiments of self-assembly of 10 nm Au nano particles (NPs), functionalized by a dense layer of azobenzene-bithiophene (AzBT) molecules, with the aim of building a light-switchable device with memristive properties. We fabricate planar nanodevices consisting of NP self-assembled network (NPSANs) contacted by nanoelectrodes separated by interelectrode gaps ranging from 30 to 100 nm. We demonstrate the light-induced reversible switching of the electrical conductance in these AzBT NPSANs with a record on/off conductance ratio up to 620, an average value of ca. 30 and with 85% of the devices having a ratio above 10. Molecular dynamics simulation of the structure and dynamics of the interface between molecular monolayers chemisorbed on the nano particle surface are performed and compared to the experimental findings. The properties of the contact interface are shown to be strongly correlated to the molecular conformation which in the case of AzBT molecules, can reversibly switched between a cis and a trans form by means of light irradiations of well-defined wavelength. Molecular dynamics simulations provide a microscopic explanation for the experimental observation of the reduction of the on/off current ratio between the two isomers, compared to experiments performed on flat self-assembled monolayers contacted by a conducting cAFM tip.Comment: pdf files : publication and supporting informatio

AGENT-BASED GENETIC MULTICELLULAR 3D MODELLING OF STEM-CELL SPHEROIDS(GENESPHERE)

International audienc

Agent-based model of multicellular tumor spheroid evolution including cell metabolism

Computational models aiming at the spatio-temporal description of cancer evolution are a suitable framework for testing biological hypotheses from experimental data, and generating new ones. Building on our recent work (J. Theor. Biol. 389, 146 (2016)) we develop a 3D agent-based model, capable of tracking hundreds of thousands of interacting cells, over time scales ranging from seconds to years. Cell dynamics is driven by a Monte Carlo solver, incorporating partial differential equations to describe chemical pathways and the activation/repression of “genes”, leading to the up- or down-regulation of specific cell markers. Each cell-agent of different kind (stem, cancer, stromal etc.) runs through its cycle, undergoes division, can exit to a dormant, senescent, necrotic state, or apoptosis, according to the inputs from its systemic network. The basic network at this stage describes glucose/oxygen/ATP cycling, and can be readily extended to cancer-cell specific markers. Eventual accumulation of chemical/radiation damage to each cell’s DNA is described by a Markov chain of internal states, and by a damage-repair network, whose evolution is linked to the cell systemic network. Aimed at a direct comparison with experiments of tumorsphere growth from stem cells, the present model will allow to quantitatively study the role of transcription factors involved in the reprogramming and variable radio-resistance of simulated cancer-stem cells, evolving in a realistic computer simulation of a growing multicellular tumorsphere

The physics of living systems

In this book, physics in its many aspects (thermodynamics, mechanics, electricity, fluid dynamics) is the guiding light on a fascinating journey through biological systems, providing ideas, examples and stimulating reflections for undergraduate physics, chemistry and life-science students, as well as for anyone interested in the frontiers between physics and biology. Rather than introducing a lot of new information, it encourages young students to use their recently acquired knowledge to start seeing the physics behind the biology. As an undergraduate textbook in introductory biophysics, it includes the necessary background and tools, including exercises and appendices, to form a progressive course. In this case, the chapters can be used in the order proposed, possibly split between two semesters. The book is also an absorbing read for researchers in the life sciences who wish to refresh or go deeper into the physics concepts gleaned in their early years of scientific training. Less physics-oriented readers might want to skip the first chapter, as well as all the "gray boxes" containing the more formal developments, and create their own á-la-carte menu of chapters