publication and news

news/_posts/2024-07-29-VikingClass.md

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+---
+layout: news
+title: 'New Publication: A Computer Laboratory for the Calculation of the Heat Capacity of a Peptide Unfolding Transition'
+excerpt: "The Biophysicist (2024)" 
+image:
+  feature: banner.png
+---
+
+## A Computer Laboratory for the Calculation of the Heat Capacity of a Peptide Unfolding Transition
+
+Lau Blom Grøndahl, **Fabian Schuhmann**, Dennis Bruhn, Vikas Dubey, Ilia A. Solov’yov, Himanshu Khandelia
+
+<b>Abstract: </b>
+We present the implementation of a computer simulation laboratory for the calculation of the heat capacity of the folding-unfolding pseudo phase transition of a polyalanine Ala30α-helix, using molecular dynamics simulations. Unlike conventional calorimetry experiments, which provide a macroscopic interpretation of the heat capacity, the computer laboratory additionally offers a molecular perspective of the energy exchange processes that lead to the peak of the heat capacity at the phase transition, as well as the statistical mechanical interpretation of the phase transition. The exercise is targeted toward 1st- or 2nd-year students of biophysics in the context of an undergraduate physical chemistry course. We use a graphical web interface to overcome the steep learning barriers associated with command line interactions in commonly used molecular dynamics protocols. The web interface (VIKING) also handles communication with computing hardware in the background, so that students with limited or no programming experience can launch and analyze the simulations easily. A collaboration between the VIKING support team and responsible teachers is required to set up VIKING. We also present a solution in which simulations can be launched on students’ own computers, if some command line knowledge can be expected. The laboratory can also be repurposed for students of various backgrounds (physics, chemistry, biology, or engineering) and scholastic levels (undergraduate or graduate).
+

news/_posts/2024-07-30-advancedworkshop.md

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+---
+layout: news
+title: 'Upcoming Workshop: Advances in Molecular Modelling from 09-10-12-2024'
+excerpt: "Registration is open, limited seats" 
+image:
+  feature: banner.png
+---
+
+## Advances in MolecularAdvances in Molecular Modelling
+
+Sign up is available [here](https://indico.nbi.ku.dk/event/2076/)
+
+![Announcement Poster](/images/posts/workshop2024.jpg)

news/_posts/2024-08-01-NegativeEigenvalues.md

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+---
+layout: news
+title: 'New Publication: Spurious negative eigenvalues of numerical variance-covariance matrices in many-body systems correlate with the existence of frozen degrees of freedom'
+excerpt: "Physica Scripta (2024)" 
+image:
+  feature: banner.png
+---
+
+## Spurious negative eigenvalues of numerical variance-covariance matrices in many-body systems correlate with the existence of frozen degrees of freedom
+
+Jonathan Hungerland, Ilia A. Solov'yov, **Fabian Schuhmann**
+
+<b>Abstract: </b>
+The principal component analysis (PCA) is widely used to reduce the dimensionality of a dataset to its essential components. To perform PCA, the covariance matrix is constructed and its eigenvalues and eigenvectors are computed. In practical numerical applications, the tail of the sorted eigenvalues is sometimes found to contain negative eigenvalues, which are prohibited mathematically and are a pure consequence of finite-accuracy numerics. The present study suggests that in the case of a many-body dynamical system, the spurious negative eigenvalues of the covariance matrix may in fact be related to the frozen degrees of freedom in the system. Here, we outline the mathematical connection between the eigenvalues of the covariance matrix and the frozen degrees of freedom and validate the connection through two case studies: a model system of coupled harmonic oscillators and a molecular dynamics simulation of a small protein in solution.
+