The 90 degree uphill turn off the Hope Valley onto the MML round the Dore curve through Dore Tunnel is one of the less well appreciated factors in the scheme. That used to be double track and is quite a tight turn. There used to be much squealing of wheels as some wagons clearly found it so. The new loop leading to it at Dore may not be long enough for the longest trains now being planned. It was originally thought possible to make it longer by demolishing some flats at West View. That would have added a lot more expense, aroused even more local opposition than running the loop right up to their car park, and was dropped even before the first round of public consultation. The Bamford loop is to be longer.
There is no easy way to avoid potential conflicts when a heavy load of cement or limestone is dragged round the curve to head south. That causes delays to both north and southbound MML traffic unless everything presents itself exactly as planned. A grade separated junction would be ideal, but incredibly expensive to construct even if it could be engineered! Think on.
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Signalling is another factor. Although the scheme includes transfer of control from Earles to York from Manchester, thereby potentially improving control over the Dore junctions, there will be no change in the blocks. Line speeds will not be improved and as I currently understand it 185s will be unable to use their full capabilities, 158s currently being able to run faster in the Hope Valley due to lighter weight.
Dore Curve, or the traffic using it at least, is a big problem and loops at Bamford alone won't sort it. The problem is that a loaded freight train from the Hope Valley has to fit into a suitable margin on the busy (and fast) line south towards Chesterfield, but also needs gaps in both traffic from Chesterfield and towards the Hope Valley to do so, and it all has to line up at once unless it's short enough to stand on the curve (and it can't even do that without a gap in trains from Chesterfield because the overlap extends over the junction). It's almost inevitable that something's going to get knocked by it, e.g. the following train heading south because it's had to be run with insufficient margin to get it out of the way of the following train off the Hope Valley. The ability to put them away at Bamford, and bringing it all under York's "control" won't help much, because things can and do change a lot in the time that it takes to get from a standing start at Bamford to passing Dore. Even if you can identify a suitable margin to run it, a passenger train delayed by just four or five minutes at Sheffield could upset the whole plan. I don't have much confidence in their ability to make such tight and distant decisions with their almost complete reliance on ARS, in any case!
The only way to really deal with it is to provide enough room to stand the longest train inside clear on the curve, so that it can be kept out of the way until a suitable margin is available to run it. I'm not sure whether the current proposal provides that, although it does at least appear to extend the curve considerably.
Going westwards a fast passenger service will still be unable to pass a stopper between the Heeley loop and after Chinley. Whether the Bamford loop will be used to allow a fast to overtake a stopper is a subject of interest. Who makes that decision and how do the penalties get passed around when the already late stopper has to take another 5 minute hit?
As always, when one bottleneck is eased the pressure starts building further along the line. Like 60mph restrictions on 3 long tunnels.
Network Rail makes the decision, either the Signalman directly or the Train Running Controller, with the objective of minimising the overall delay. As with the example of Glazebrook, which is where the CLC stopper invariably gets recessed when the Norwich - Liverpool service is late because it's been hammered over the Hope Valley, putting the stopper inside for a few minutes would usually be preferable to keeping it out and delaying the following fast by many more minutes.
None of the three tunnels have a 60mph restriction?
Shorter signal blocks would help massively as some of them are immensely huge. Not only that, but the heavily-talked about of the splitting of Norwich-Liverpool would need to be a priority to alleviate delay. There's far too many pinch points to incumbere the Hope Valley at the moment.
As Edwin_m suggests, splitting the Norwich - Liverpool service won't help much. It has some recovery time at Nottingham (and approaching Sheffield) to cope with minor delays without destroying the 'connection' for through passengers, and it's common for it to be 'restarted' right-time at Nottingham if the inward from Norwich is significantly delayed.
The longest block sections over there are Totley Tunnel East - Grindleford and Edale - Chinley, and in neither case is the section very much longer than the tunnel in the middle of it (so you can't shorten the section by much without introducing stop signals in the tunnel itself). You'd be able to squeeze a couple of minutes, perhaps, with shorter sections but that won't help much when there's such a big differential between the average speed of the stopping passengers and freights, and the average speed of the fasts.