Related papers: Single-molecule force spectroscopy reveals structu…
There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is dynamically…
Tautomerization is a fast chemical reaction where structures of the reactants differ only in the position of a proton and a double bond. Tautomerization often occurs in natural substances and is a fundamental process in organic- and…
Access to high-energy particle beams is key for testing high-energy physics (HEP) instruments. Accelerators for cancer treatment can serve as such a testing ground. However, HEP instrument tests typically require particle fluxes…
Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule F\"orster resonance energy transfer (smFRET) provides access to enzymatically important timescales, combined with molecular…
We have studied the electronic properties, in relation to their structural properties, of monolayers of 1-octadecene attached on a hydrogen-terminated (111) silicon surface. The molecules are attached using the free-radical reaction between…
We introduce a machine learning approach to determine the transition dynamics of silicon atoms on a single layer of carbon atoms, when stimulated by the electron beam of a scanning transmission electron microscope (STEM). Our method is…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
Recent experiment on MoTe$_2$-WTe$_2$ twisted bi-layer demonstrated physics of Kane-Mele (KM) as well as Haldane models. Although topological properties of KM model has been studied extensively, effects of interaction are still less…
Abnormal metabolism is an emerging hallmark of cancer. Cancer cells utilize both aerobic glycolysis and oxidative phosphorylation (OXPHOS) for energy production and biomass synthesis. Understanding the metabolic reprogramming in cancer can…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows…
Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…
Epidermal growth factor (EGF), a potent cytokine, is known to promote tumor invasion both in vivo and in vitro. Previously, we observed that single breast tumor cells (MDA-MB-231 cell line) embedded within a 3D collagen matrix displayed…
Precision spectroscopy on cold molecules can potentially enable novel tests of fundamental laws of physics and alternative determination of some fundamental constants. Realizing this potential requires a thorough understanding of the…
Graphyne is a generic name for a carbon allotrope family of 2D structures, where acetylenic groups connect benzenoid rings, with the coexistence of sp and sp2 hybridized carbon atoms. In this work we have investigated, through fully…
The design of hybrid peptide-solid interfaces for nanotechnological applications such as biomolecular nanoarrays requires a deep understanding of the basic mechanisms of peptide binding and assembly at solid substrates. Here we show by…
The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via…
The immune checkpoint inhibitors have demonstrated promising clinical efficacy across various tumor types, yet the percentage of patients who benefit from them remains low. The bindings between tumor antigens and HLA-I/TCR molecules…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…