Quantum and Classical Molecular Dynamics

PGR-P-109

Key facts

Type of research degree: PhD
Application deadline: Ongoing deadline
Country eligibility: International (open to all nationalities, including the UK)
Funding: Competition funded
Supervisors: Professor Dmitry Shalashilin
Schools: School of Chemistry

<h2 class="heading hide-accessible">Summary</h2>

There are two main research projects available. First project is focused on quantum dynamics in chemistry and physics. Second project is focused on classical Molecular Dynamics (MD) of biological molecules such as proteins and peptides 1 Chemistry is about rearranging nuclei whose motion is often quantum. Understanding tunnelling, zero point energy, quantization of vibrational and rotational motions and transitions between electronic states is crucial for chemical dynamics. We develop new techniques which speed up quantum simulations and allow to treat larger molecular systems 1-3. The main idea is to use classical mechanics to guide quantum basis, which is illustrated on the figure below showing a trajectory guided grid following the wave function 2 Classical MD disregards quantum effects but can treat realistic molecular systems comprised of thousands of atoms. The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude has to be bridged. We developed efficient methods which allow to solve this problem by recovering long time dynamics from a set of short time simulations.

<h2 class="heading hide-accessible">Full description</h2>

In 1929 Dirac stated that: “<a href="http://www.brainyquote.com/quotes/quotes/p/pauldirac279318.html" title="view quote">The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved.</a>” Only recently however, many years later, have atomistic simulation methods started to emerge that allow the treatment of quantum systems with many degrees of freedom, overcoming the difficulty noted by Dirac. Leeds Quantum and Classical Molecular Dynamics group develops new computational methods for atomistic simulations in chemistry and physics.  These methods can treat bigger molecular systems faster and more accurately.  They can visualise what happens at in atomic and molecular level.   There are two main research projects available. First project is focused on quantum dynamics in chemistry and physics. Chemistry is about rearranging nuclei whose motion is often quantum.  Understanding tunnelling, zero point energy, quantization of vibrational and rotational motions and transitions between electronic states is crucial for chemical dynamics.  We develop new techniques which speed up quantum simulations and allow to treat larger molecular systems1-3.  The main idea is to use classical mechanics to guide quantum basis, which is illustrated on the figure below showing a trajectory guided grid following the wave function We developed several methods, which exploit this very simple idea, and applied them to many interesting problems in chemistry and physics which range from chemical dynamics on ultrafast femtosecond time scale to dynamics of electrons in laser field and even quantum computers. Second project is focused on classical Molecular Dynamics (MD) of biological molecules such as proteins and peptides.  Classical MD disregards quantum effects but can treat realistic molecular systems comprised of thousands of atoms.  The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude has to be bridged.  We developed efficient methods which allow to solve this problem by recovering long time dynamics from  a set of short time simulations.    We apply our methods of accelerated classical MD to the investigation of protein unfolding, and peptide cyclization.  For example with the help of our new methods we work on computational design of cyclic peptides, which currently are considered as prospective new antibiotics and anticancer drugs. Our research is very mathematical and involves the use of powerful computers.  Both projects are suited not only for chemists but also for physics and mathematics graduates.  Further information about our <a href="Quantum and Classical Molecular Dynamics Project">Quantum and Classical Molecular Dynamics Project</a> (PDF) The earliest start date for this project will be 1 October 2020.

<h2 class="heading">How to apply</h2>

Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/info/130206/applying/91/applying_for_research_degrees">University's website</a>. Please state clearly in the Planned Course of Study that you are applying for PHD Chemistry FT and in the research information section that the research degree you wish to be considered for is Quantum and Classical Molecular Dynamics as well as <a href="https://physicalsciences.leeds.ac.uk/staff/197/professor-dmitry-shalashilin">Professor Dmitry Shalashilin</a> as your proposed supervisor. If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below). As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability. Applications will be considered on an ongoing basis.  Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application.  We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed. Please note that you must provide the following documents at the point you submit your application: <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> <li>Funding information including any alternative sources of funding that you are applying for or if you are able to pay your own fees and maintenance</li> </ul>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

Self-Funded or externally sponsored students are welcome to apply. UK – The <a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> are available to UK applicants. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Non-UK –The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China. The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Important:  Any costs associated with your arrival at the University of Leeds to start your PhD including flights, immigration health surcharge/medical insurance and Visa costs are not covered under these studentships. Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.

<h2 class="heading">Contact details</h2>

For further information about your application, please contact Doctoral College Admissions: e: <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions</a><a href="mailto:EMAIL@leeds.ac.uk">@leeds.ac.uk</a> For further information about this project, please contact Professor Dmitry Shalashilin: e:  <a href="mailto:D.Shalashilin@leeds.ac.uk">D.Shalashilin@leeds.ac.uk</a>